InPAS 1.18.0
Alternative polyadenylation (APA) is one of the most important post-transcriptional regulation mechanisms which is prevalent in human genes. Like alternative splicing, APA can create proteome diversity. In addition, it defines 3’ UTR and results in altered expression of the gene. It is a tightly controlled process and mis-regulation of APA can lead to pathological effects to the cells, such as uncontrolled cell cycle and growth. Although several high throughput sequencing methods have been developed, there are still limited data available.
RNA-seq has become one of the most commonly used methods for quantifying genome-wide gene expression. There are massive RNA-seq datasets available in public databases such as GEO and TCGA. For this reason, we develop the InPAS algorithm for identifying APA from conventional RNA-seq data.
The workflow for InPAS is:
First, load the required libraries InPAS, species specific BSgenome, and TxDb as follows.
library(InPAS)
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
path <- file.path(find.package("InPAS"), "extdata")Next, prepare annotation using the function utr3Annotation with a TxDb and org annotation.
Please note that the 3’ UTR annotation prepared by utr3Annotation
includes the gaps to the next annotated region.
library(org.Hs.eg.db)
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
package="GenomicFeatures")
txdb <- loadDb(samplefile)
utr3.sample.anno <- utr3Annotation(txdb=txdb,
orgDbSYMBOL="org.Hs.egSYMBOL")
utr3.sample.anno## GRanges object with 155 ranges and 7 metadata columns:
## seqnames ranges strand |
## <Rle> <IRanges> <Rle> |
## uc001bum.2_5|IQCC|utr3 chr1 32673684-32674288 + |
## uc001fbq.3_3|S100A9|utr3 chr1 153333315-153333503 + |
## uc001gde.2_2|LRRC52|utr3 chr1 165533062-165533185 + |
## uc001hfg.3_15|PFKFB2|utr3 chr1 207245717-207251162 + |
## uc001hfh.3_15|PFKFB2|utr3 chr1 207252365-207254368 + |
## ... ... ... ... .
## uc004dsv.3_19|PHF8|CDS chrX 53964414-53964492 - |
## uc004dsx.3_15|PHF8|CDS chrX 53969797-53969835 - |
## uc004ehz.1_5|ARMCX3|CDS chrX 100879970-100881109 + |
## uc004elw.3_6|FAM199X|CDS chrX 103434289-103434459 + |
## uc004fmj.1_10|GAB3|CDS chrX 153906455-153906571 - |
## feature annotatedProximalCP exon
## <character> <character> <character>
## uc001bum.2_5|IQCC|utr3 utr3 unknown uc001bum.2_5
## uc001fbq.3_3|S100A9|utr3 utr3 unknown uc001fbq.3_3
## uc001gde.2_2|LRRC52|utr3 utr3 unknown uc001gde.2_2
## uc001hfg.3_15|PFKFB2|utr3 utr3 unknown uc001hfg.3_15
## uc001hfh.3_15|PFKFB2|utr3 utr3 unknown uc001hfh.3_15
## ... ... ... ...
## uc004dsv.3_19|PHF8|CDS CDS unknown uc004dsv.3_19
## uc004dsx.3_15|PHF8|CDS CDS unknown uc004dsx.3_15
## uc004ehz.1_5|ARMCX3|CDS CDS unknown uc004ehz.1_5
## uc004elw.3_6|FAM199X|CDS CDS unknown uc004elw.3_6
## uc004fmj.1_10|GAB3|CDS CDS unknown uc004fmj.1_10
## transcript gene symbol truncated
## <character> <character> <character> <logical>
## uc001bum.2_5|IQCC|utr3 uc001bum.2 55721 IQCC FALSE
## uc001fbq.3_3|S100A9|utr3 uc001fbq.3 6280 S100A9 FALSE
## uc001gde.2_2|LRRC52|utr3 uc001gde.2 440699 LRRC52 FALSE
## uc001hfg.3_15|PFKFB2|utr3 uc001hfg.3 5208 PFKFB2 FALSE
## uc001hfh.3_15|PFKFB2|utr3 uc001hfh.3 5208 PFKFB2 FALSE
## ... ... ... ... ...
## uc004dsv.3_19|PHF8|CDS uc004dsv.3 23133 PHF8 FALSE
## uc004dsx.3_15|PHF8|CDS uc004dsx.3 23133 PHF8 FALSE
## uc004ehz.1_5|ARMCX3|CDS uc004ehz.1 51566 ARMCX3 FALSE
## uc004elw.3_6|FAM199X|CDS uc004elw.3 139231 FAM199X FALSE
## uc004fmj.1_10|GAB3|CDS uc004fmj.1 139716 GAB3 FALSE
## -------
## seqinfo: 27 sequences from hg19 genome; no seqlengthsUsers can also directly load the 3’ UTR annotation included in this package for mm10 and hg19. Here we show how to load the pre-built mm10 3’ UTR annotation file.
##step1 annotation
# load from dataset
data(utr3.mm10)For coverage calculation, alignment files in BEDGraph format are required, which can be generated from BAM files using the genomecov tool in bedtools with parameter: -bg -split. Potential pA sites identified from the coverage data can be filtered/adjusted using the classifier provided by cleanUpdTseq. The following scripts illustrate the function calls needed to perform the complete analysis using InPAS.
load(file.path(path, "polyA.rds"))
library(cleanUpdTSeq)
data(classifier)
bedgraphs <- c(file.path(path, "Baf3.extract.bedgraph"),
file.path(path, "UM15.extract.bedgraph"))
hugeData <- FALSE
##step1 Calculate coverage
coverage <- coverageFromBedGraph(bedgraphs,
tags=c("Baf3", "UM15"),
genome=BSgenome.Mmusculus.UCSC.mm10,
hugeData=hugeData)
## we hope the coverage rate of should be greater than 0.75 in the expressed gene.
## which is used because the demo data is a subset of genome.
coverageRate(coverage=coverage,
txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
genome=BSgenome.Mmusculus.UCSC.mm10,
which = GRanges("chr6", ranges=IRanges(98013000, 140678000)))## strand information will be ignored.## gene.coverage.rate expressed.gene.coverage.rate UTR3.coverage.rate
## Baf3 0.01031381 0.6300834 0.01830495
## UM15 0.01020966 0.6236834 0.01846496
## UTR3.expressed.gene.subset.coverage.rate
## Baf3 0.8082201
## UM15 0.8152853##step2 Predict cleavage sites
CPs <- CPsites(coverage=coverage,
genome=BSgenome.Mmusculus.UCSC.mm10,
utr3=utr3.mm10,
search_point_START=200,
cutEnd=.2,
long_coverage_threshold=3,
background="10K",
txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
PolyA_PWM=pwm,
classifier=classifier,
shift_range=50,
step=10)
head(CPs)## GRanges object with 4 ranges and 12 metadata columns:
## seqnames ranges strand |
## <Rle> <IRanges> <Rle> |
## uc009daz.2_10|Mitf|utr3 chr6 98018176-98021358 + |
## uc009dhz.2_19|Atg7|utr3 chr6 114859343-114860614 + |
## uc009dmb.2_4|Lrtm2|utr3 chr6 119315133-119317055 - |
## uc009eet.1_3|BC035044|utr3 chr6 128848044-128850081 - |
## annotatedProximalCP exon transcript
## <character> <character> <character>
## uc009daz.2_10|Mitf|utr3 unknown uc009daz.2_10 uc009daz.2
## uc009dhz.2_19|Atg7|utr3 unknown uc009dhz.2_19 uc009dhz.2
## uc009dmb.2_4|Lrtm2|utr3 unknown uc009dmb.2_4 uc009dmb.2
## uc009eet.1_3|BC035044|utr3 unknown uc009eet.1_3 uc009eet.1
## gene symbol truncated
## <character> <character> <logical>
## uc009daz.2_10|Mitf|utr3 17342 Mitf FALSE
## uc009dhz.2_19|Atg7|utr3 74244 Atg7 FALSE
## uc009dmb.2_4|Lrtm2|utr3 211187 Lrtm2 FALSE
## uc009eet.1_3|BC035044|utr3 232406 BC035044 FALSE
## fit_value Predicted_Proximal_APA
## <numeric> <numeric>
## uc009daz.2_10|Mitf|utr3 12594.6737481599 98018978
## uc009dhz.2_19|Atg7|utr3 27383.4125399619 114859674
## uc009dmb.2_4|Lrtm2|utr3 168.550899294257 119316541
## uc009eet.1_3|BC035044|utr3 123.973723777853 128849177
## Predicted_Distal_APA type utr3start
## <numeric> <character> <numeric>
## uc009daz.2_10|Mitf|utr3 98021358 novel proximal 98018276
## uc009dhz.2_19|Atg7|utr3 114862071 novel distal 114859443
## uc009dmb.2_4|Lrtm2|utr3 119315133 novel proximal 119316955
## uc009eet.1_3|BC035044|utr3 128846744 novel distal 128849981
## utr3end
## <numeric>
## uc009daz.2_10|Mitf|utr3 98021358
## uc009dhz.2_19|Atg7|utr3 114860614
## uc009dmb.2_4|Lrtm2|utr3 119315133
## uc009eet.1_3|BC035044|utr3 128848044
## -------
## seqinfo: 42 sequences from mm10 genome; no seqlengths##step3 Estimate 3UTR usage
res <- testUsage(CPsites=CPs,
coverage=coverage,
genome=BSgenome.Mmusculus.UCSC.mm10,
utr3=utr3.mm10,
method="fisher.exact",
gp1="Baf3", gp2="UM15")
##step4 view the results
as(res, "GRanges") ## GRanges object with 4 ranges and 27 metadata columns:
## seqnames ranges strand | annotatedProximalCP
## <Rle> <IRanges> <Rle> | <character>
## uc009daz.2 chr6 98018176-98021358 + | unknown
## uc009dhz.2 chr6 114859343-114862071 + | unknown
## uc009dmb.2 chr6 119315133-119317055 - | unknown
## uc009eet.1 chr6 128846744-128850081 - | unknown
## transcript gene symbol truncated fit_value
## <character> <character> <character> <logical> <numeric>
## uc009daz.2 uc009daz.2 17342 Mitf FALSE 12594.6737481599
## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 27383.4125399619
## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 168.550899294257
## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 123.973723777853
## Predicted_Proximal_APA Predicted_Distal_APA type
## <numeric> <numeric> <character>
## uc009daz.2 98018978 98021358 novel proximal
## uc009dhz.2 114859674 114862071 novel distal
## uc009dmb.2 119316541 119315133 novel proximal
## uc009eet.1 128849177 128846744 novel distal
## utr3start utr3end Baf3_short.form.usage UM15_short.form.usage
## <numeric> <numeric> <numeric> <numeric>
## uc009daz.2 98018276 98021358 33.5313380764804 1.05214965526127
## uc009dhz.2 114859443 114860614 520.914790102864 172.152349179872
## uc009dmb.2 119316955 119315133 8.85786481015595 49.5356159541359
## uc009eet.1 128849981 128848044 21.6461685265195 0
## Baf3_long.form.usage UM15_long.form.usage Baf3_PDUI
## <numeric> <numeric> <numeric>
## uc009daz.2 282.82402351953 189.141117177656 0.894007365933945
## uc009dhz.2 208.02460383653 456.544620517098 0.285379834820432
## uc009dmb.2 8.53513129879347 70.8126330731015 0.490722314046962
## uc009eet.1 8.90221857025472 23.2912900575185 0.291413701877399
## UM15_PDUI short.mean.gp1 long.mean.gp1
## <numeric> <numeric> <numeric>
## uc009daz.2 0.994467997354577 33.5313380764804 282.82402351953
## uc009dhz.2 0.726175952044354 520.914790102864 208.02460383653
## uc009dmb.2 0.588397701216867 8.85786481015595 8.53513129879347
## uc009eet.1 1 21.6461685265195 8.90221857025472
## short.mean.gp2 long.mean.gp2 PDUI.gp1
## <numeric> <numeric> <numeric>
## uc009daz.2 1.05214965526127 189.141117177656 0.894007365933945
## uc009dhz.2 172.152349179872 456.544620517098 0.285379834820432
## uc009dmb.2 49.5356159541359 70.8126330731015 0.490722314046962
## uc009eet.1 0 23.2912900575185 0.291413701877399
## PDUI.gp2 dPDUI logFC
## <numeric> <numeric> <numeric>
## uc009daz.2 0.994467997354577 -0.100460631420632 -0.153638226758031
## uc009dhz.2 0.726175952044354 -0.440796117223922 -1.34743575844534
## uc009dmb.2 0.588397701216867 -0.0976753871699045 -0.261884735309782
## uc009eet.1 1 -0.708586298122601 -1.77885938232419
## P.Value adj.P.Val
## <numeric> <numeric>
## uc009daz.2 1.58697962749085e-06 2.11597283665446e-06
## uc009dhz.2 1.7094761107206e-60 6.8379044428824e-60
## uc009dmb.2 0.593030861268587 0.593030861268587
## uc009eet.1 4.13501327860387e-08 8.27002655720775e-08
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengthsfilterRes(res, gp1="Baf3", gp2="UM15",
background_coverage_threshold=3,
adj.P.Val_cutoff=0.05,
dPDUI_cutoff=0.3,
PDUI_logFC_cutoff=0.59)## GRanges object with 4 ranges and 28 metadata columns:
## seqnames ranges strand | annotatedProximalCP
## <Rle> <IRanges> <Rle> | <character>
## uc009daz.2 chr6 98018176-98021358 + | unknown
## uc009dhz.2 chr6 114859343-114862071 + | unknown
## uc009dmb.2 chr6 119315133-119317055 - | unknown
## uc009eet.1 chr6 128846744-128850081 - | unknown
## transcript gene symbol truncated fit_value
## <character> <character> <character> <logical> <numeric>
## uc009daz.2 uc009daz.2 17342 Mitf FALSE 12594.6737481599
## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 27383.4125399619
## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 168.550899294257
## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 123.973723777853
## Predicted_Proximal_APA Predicted_Distal_APA type
## <numeric> <numeric> <character>
## uc009daz.2 98018978 98021358 novel proximal
## uc009dhz.2 114859674 114862071 novel distal
## uc009dmb.2 119316541 119315133 novel proximal
## uc009eet.1 128849177 128846744 novel distal
## utr3start utr3end Baf3_short.form.usage UM15_short.form.usage
## <numeric> <numeric> <numeric> <numeric>
## uc009daz.2 98018276 98021358 33.5313380764804 1.05214965526127
## uc009dhz.2 114859443 114860614 520.914790102864 172.152349179872
## uc009dmb.2 119316955 119315133 8.85786481015595 49.5356159541359
## uc009eet.1 128849981 128848044 21.6461685265195 0
## Baf3_long.form.usage UM15_long.form.usage Baf3_PDUI
## <numeric> <numeric> <numeric>
## uc009daz.2 282.82402351953 189.141117177656 0.894007365933945
## uc009dhz.2 208.02460383653 456.544620517098 0.285379834820432
## uc009dmb.2 8.53513129879347 70.8126330731015 0.490722314046962
## uc009eet.1 8.90221857025472 23.2912900575185 0.291413701877399
## UM15_PDUI short.mean.gp1 long.mean.gp1
## <numeric> <numeric> <numeric>
## uc009daz.2 0.994467997354577 33.5313380764804 282.82402351953
## uc009dhz.2 0.726175952044354 520.914790102864 208.02460383653
## uc009dmb.2 0.588397701216867 8.85786481015595 8.53513129879347
## uc009eet.1 1 21.6461685265195 8.90221857025472
## short.mean.gp2 long.mean.gp2 PDUI.gp1
## <numeric> <numeric> <numeric>
## uc009daz.2 1.05214965526127 189.141117177656 0.894007365933945
## uc009dhz.2 172.152349179872 456.544620517098 0.285379834820432
## uc009dmb.2 49.5356159541359 70.8126330731015 0.490722314046962
## uc009eet.1 0 23.2912900575185 0.291413701877399
## PDUI.gp2 dPDUI logFC
## <numeric> <numeric> <numeric>
## uc009daz.2 0.994467997354577 -0.100460631420632 -0.153638226758031
## uc009dhz.2 0.726175952044354 -0.440796117223922 -1.34743575844534
## uc009dmb.2 0.588397701216867 -0.0976753871699045 -0.261884735309782
## uc009eet.1 1 -0.708586298122601 -1.77885938232419
## P.Value adj.P.Val PASS
## <numeric> <numeric> <logical>
## uc009daz.2 1.58697962749085e-06 2.11597283665446e-06 FALSE
## uc009dhz.2 1.7094761107206e-60 6.8379044428824e-60 TRUE
## uc009dmb.2 0.593030861268587 0.593030861268587 FALSE
## uc009eet.1 4.13501327860387e-08 8.27002655720775e-08 TRUE
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengthsThe steps described above can be done in one function call.
if(interactive()){
res <- inPAS(bedgraphs=bedgraphs, tags=c("Baf3", "UM15"),
genome=BSgenome.Mmusculus.UCSC.mm10,
utr3=utr3.mm10, gp1="Baf3", gp2="UM15",
txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
search_point_START=200,
short_coverage_threshold=15,
long_coverage_threshold=3,
cutStart=0, cutEnd=.2,
hugeData=FALSE,
shift_range=50,
PolyA_PWM=pwm, classifier=classifier,
method="fisher.exact",
adj.P.Val_cutoff=0.05,
dPDUI_cutoff=0.3,
PDUI_logFC_cutoff=0.59)
}InPAS can also handle single group data.
inPAS(bedgraphs=bedgraphs[1], tags=c("Baf3"),
genome=BSgenome.Mmusculus.UCSC.mm10,
utr3=utr3.mm10, gp1="Baf3", gp2=NULL,
txdb=TxDb.Mmusculus.UCSC.mm10.knownGene,
search_point_START=200,
short_coverage_threshold=15,
long_coverage_threshold=3,
cutStart=0, cutEnd=.2,
hugeData=FALSE,
PolyA_PWM=pwm, classifier=classifier,
method="singleSample",
adj.P.Val_cutoff=0.05,
step=10)## converged at iteration 1 with logLik: -1835.501
## converged at iteration 5 with logLik: -838.8306
## converged at iteration 1 with logLik: -1496.738
## converged at iteration 13 with logLik: -724.6964
## converged at iteration 1 with logLik: -997.3022
## converged at iteration 15 with logLik: -553.6445
## converged at iteration 1 with logLik: -188.938
## converged at iteration 23 with logLik: -152.6663
## converged at iteration 1 with logLik: -462.3804
## converged at iteration 10 with logLik: -214.1651## dPDUI is calculated by gp2 - gp1.## GRanges object with 6 ranges and 22 metadata columns:
## seqnames ranges strand | annotatedProximalCP
## <Rle> <IRanges> <Rle> | <character>
## uc009daz.2 chr6 98018176-98021358 + | unknown
## uc009dhz.2 chr6 114859343-114862075 + | unknown
## uc009die.2 chr6 114860617-114862164 - | unknown
## uc009dmb.2 chr6 119315133-119317055 - | unknown
## uc009eet.1 chr6 128847265-128850081 - | unknown
## uc009eol.1 chr6 140651362-140651622 + | unknown
## transcript gene symbol truncated fit_value
## <character> <character> <character> <logical> <numeric>
## uc009daz.2 uc009daz.2 17342 Mitf FALSE 17843.7079181186
## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 7630.49809358993
## uc009die.2 uc009die.2 232334 Vgll4 FALSE 10704.6989063837
## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 18.635065106255
## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 227.54183333935
## uc009eol.1 uc009eol.1 11569 Aebp2 TRUE 204539.698420888
## Predicted_Proximal_APA Predicted_Distal_APA type
## <numeric> <numeric> <character>
## uc009daz.2 98019022 98021358 novel proximal
## uc009dhz.2 114860283 114862075 novel distal
## uc009die.2 114861446 114860617 novel distal
## uc009dmb.2 119316683 119315133 novel proximal
## uc009eet.1 128848843 128847265 novel distal
## uc009eol.1 140651566 140651622 novel proximal
## utr3start utr3end
## <numeric> <numeric>
## uc009daz.2 98018176 98021358
## uc009dhz.2 114859343 114860614
## uc009die.2 114862164 114862092
## uc009dmb.2 119317055 119315133
## uc009eet.1 128850081 128848044
## uc009eol.1 140651362 140651622
## data2
## <list>
## uc009daz.2 c(473, 460, 457, 450, 442, 436, 433, 435, 435, 431, 421, 420, 422, 423, 422, 422, 416, 417, 416, 417, 412, 416, 421, 424, 418, 408, 417, 406, 414, 415, 411, 402, 403, 393, 362, 348, 295, 266, 232, 230, 228, 224, 219, 216, 208, 206, 206, 205, 196, 196, 198, 197, 197, 199, 200, 197, 209, 213, 212, 211, 210, 213, 203, 204, 209, 207, 215, 216, 216, 215, 215, 215, 215, 206, 206, 206, 203, 205, 205, 206, 205, 203, 199, 199, 195, 193, 189, 196, 194, 194, 201, 203, 204, 202, 209, 211, 214, 220, 220, 220, \n221, 221, 221, 216, 215, 214, 214, 206, 205, 205, 208, 208, 203, 208, 208, 204, 204, 205, 205, 206, 204, 201, 198, 200, 198, 236, 224, 211, 203, 200, 203, 198, 195, 199, 199, 197, 196, 198, 198, 196, 196, 198, 200, 202, 201, 203, 214, 217, 217, 218, 218, 219, 220, 216, 215, 215, 202, 200, 200, 206, 206, 204, 201, 201, 196, 209, 201, 200, 204, 208, 208, 208, 208, 208, 208, 208, 208, 209, 209, 209, 224, 225, 225, 225, 226, 226, 226, 221, 221, 225, 218, 218, 218, 219, 213, 212, 213, 206, 209, 209, 213, \n235, 236, 234, 239, 246, 248, 262, 271, 282, 280, 282, 290, 284, 285, 285, 289, 299, 300, 301, 301, 301, 300, 296, 296, 254, 252, 252, 252, 259, 267, 266, 268, 268, 277, 282, 283, 289, 292, 291, 295, 294, 301, 303, 304, 306, 308, 307, 308, 324, 323, 342, 346, 347, 356, 355, 356, 358, 358, 352, 351, 351, 350, 350, 351, 338, 338, 345, 341, 337, 338, 340, 340, 340, 340, 339, 340, 336, 336, 334, 319, 317, 317, 315, 319, 319, 321, 319, 319, 315, 319, 316, 315, 314, 313, 319, 344, 360, 365, 363, 382, 366, \n366, 361, 362, 353, 356, 342, 334, 323, 322, 319, 313, 317, 325, 327, 323, 317, 324, 321, 321, 317, 321, 325, 325, 325, 329, 332, 328, 334, 323, 323, 322, 328, 320, 317, 318, 317, 317, 313, 323, 319, 313, 310, 318, 319, 306, 306, 306, 288, 288, 276, 273, 274, 268, 268, 269, 266, 266, 266, 266, 265, 266, 266, 269, 271, 270, 264, 264, 271, 270, 268, 274, 274, 287, 287, 286, 286, 286, 286, 286, 292, 293, 294, 291, 292, 290, 290, 291, 294, 292, 292, 294, 293, 300, 302, 275, 258, 250, 251, 229, 226, 225, \n225, 224, 225, 225, 229, 229, 231, 235, 235, 233, 230, 221, 220, 227, 221, 214, 214, 216, 215, 212, 206, 206, 206, 202, 198, 198, 197, 196, 204, 209, 202, 225, 226, 226, 219, 220, 220, 212, 223, 239, 242, 234, 234, 233, 233, 237, 241, 249, 252, 251, 257, 254, 255, 255, 266, 270, 282, 282, 283, 282, 282, 279, 279, 286, 298, 307, 310, 312, 328, 328, 334, 321, 323, 343, 349, 359, 364, 371, 365, 367, 381, 386, 387, 388, 388, 387, 384, 383, 387, 392, 390, 397, 391, 392, 392, 407, 407, 413, 411, 412, 413, \n409, 408, 408, 413, 417, 417, 414, 434, 438, 439, 440, 443, 435, 443, 457, 458, 462, 464, 462, 470, 470, 472, 472, 481, 482, 476, 490, 481, 481, 477, 452, 451, 451, 453, 450, 454, 453, 444, 428, 427, 427, 426, 430, 440, 442, 439, 434, 422, 425, 418, 425, 427, 439, 431, 429, 425, 428, 427, 431, 430, 436, 434, 431, 420, 411, 404, 406, 394, 390, 389, 389, 386, 366, 360, 352, 347, 342, 348, 345, 337, 332, 330, 337, 337, 338, 338, 338, 340, 357, 364, 357, 359, 392, 402, 388, 396, 388, 393, 401, 400, 400, \n400, 399, 393, 390, 394, 395, 381, 377, 376, 378, 380, 386, 382, 368, 367, 362, 361, 361, 355, 356, 373, 375, 368, 366, 375, 362, 361, 360, 366, 371, 385, 384, 383, 384, 379, 379, 377, 377, 376, 380, 403, 397, 391, 403, 404, 406, 417, 417, 425, 420, 417, 407, 413, 415, 428, 447, 451, 450, 453, 466, 467, 467, 467, 469, 466, 466, 460, 462, 457, 464, 468, 468, 469, 469, 479, 501, 502, 509, 502, 502, 504, 497, 498, 497, 499, 502, 502, 478, 472, 465, 459, 425, 418, 421, 413, 413, 407, 400, 405, 405, 405, \n408, 404, 403, 401, 403, 396, 397, 401, 398, 393, 388, 388, 386, 386, 385, 387, 386, 391, 394, 376, 374, 373, 376, 363, 363, 364, 361, 356, 353, 341, 356, 359, 359, 359, 362, 362, 369, 366, 363, 337, 339, 342, 326, 329, 328, 333, 331, 321, 323, 323, 319, 310, 307, 289, 271, 268, 272, 272, 252, 251, 247, 248, 246, 247, 243, 243, 241, 272, 265, 265, 269, 268, 267, 259, 234, 228, 221, 221, 219, 219, 219, 220, 222, 220, 216, 210, 210, 209, 211, 211, 213, 211, 211, 215, 215, 215, 215, 210, 210, 211, 207, \n207, 210, 208, 205, 206, 205, 205, 205, 205, 204, 203, 209, 209, 210, 208, 218, 232, 231, 236, 240, 262, 292, 298, 297, 321, 320, 322, 321, 316, 303, 301, 299, 304, 303, 304, 299, 316, 318, 318)
## uc009dhz.2 c(184, 184, 184, 184, 187, 187, 188, 190, 196, 201, 208, 212, 212, 216, 217, 218, 221, 221, 222, 222, 222, 228, 228, 228, 231, 235, 236, 236, 241, 241, 243, 244, 245, 245, 245, 245, 247, 242, 243, 245, 246, 243, 248, 251, 251, 250, 236, 235, 236, 232, 224, 223, 226, 228, 227, 228, 228, 228, 232, 235, 235, 235, 234, 234, 230, 230, 235, 236, 234, 234, 245, 245, 244, 239, 239, 239, 240, 242, 231, 227, 227, 223, 219, 215, 214, 214, 213, 189, 183, 178, 180, 177, 172, 169, 169, 174, 180, 179, 177, 175, \n177, 180, 180, 183, 180, 181, 181, 181, 176, 173, 168, 168, 170, 168, 168, 171, 172, 174, 174, 175, 181, 177, 177, 182, 181, 178, 178, 184, 187, 187, 185, 186, 185, 187, 201, 201, 198, 203, 202, 198, 196, 193, 188, 186, 188, 188, 190, 190, 189, 188, 186, 188, 188, 187, 194, 194, 197, 199, 199, 198, 198, 205, 212, 213, 211, 211, 205, 206, 206, 206, 195, 209, 207, 206, 207, 207, 208, 206, 206, 209, 209, 208, 212, 216, 234, 234, 232, 235, 238, 248, 246, 251, 256, 255, 261, 257, 248, 247, 246, 244, 242, \n239, 239, 236, 242, 241, 241, 239, 244, 247, 243, 240, 241, 247, 250, 250, 251, 257, 270, 271, 277, 282, 295, 289, 295, 295, 295, 289, 282, 284, 285, 283, 292, 292, 280, 281, 283, 281, 281, 282, 285, 289, 297, 300, 302, 303, 303, 305, 305, 306, 307, 302, 303, 302, 295, 302, 300, 298, 295, 293, 293, 286, 280, 279, 278, 279, 278, 276, 277, 277, 291, 278, 285, 290, 289, 291, 291, 305, 306, 303, 303, 306, 302, 299, 282, 283, 291, 288, 283, 274, 274, 269, 263, 267, 261, 266, 266, 264, 275, 278, 279, 279, \n282, 284, 278, 278, 278, 280, 281, 281, 293, 293, 293, 285, 281, 288, 283, 275, 262, 266, 256, 255, 248, 248, 242, 241, 244, 244, 249, 247, 252, 252, 244, 242, 249, 248, 247, 252, 252, 251, 250, 251, 244, 239, 235, 234, 233, 256, 259, 259, 260, 260, 255, 255, 259, 255, 255, 258, 261, 265, 269, 273, 271, 271, 277, 276, 279, 279, 280, 284, 286, 304, 298, 293, 292, 288, 286, 269, 268, 268, 268, 277, 277, 279, 285, 284, 278, 279, 283, 286, 286, 286, 292, 288, 292, 286, 286, 286, 279, 279, 280, 280, 282, \n280, 286, 289, 288, 292, 285, 286, 283, 287, 285, 285, 300, 289, 289, 290, 290, 289, 288, 290, 285, 287, 286, 287, 284, 287, 281, 283, 277, 278, 279, 281, 298, 300, 307, 302, 310, 315, 331, 330, 329, 329, 329, 335, 338, 313, 315, 318, 316, 316, 320, 320, 316, 314, 313, 312, 308, 304, 300, 303, 303, 303, 298, 298, 295, 295, 293, 289, 276, 257, 256, 256, 256, 256, 256, 257, 267, 267, 268, 256, 256, 255, 248, 247, 245, 244, 240, 236, 236, 237, 231, 231, 231, 231, 228, 228, 224, 218, 218, 220, 219, 219, \n217, 214, 214, 208, 208, 205, 196, 191, 190, 190, 175, 175, 177, 176, 176, 172, 170, 161, 160, 157, 158, 157, 157, 154, 154, 152, 152, 151, 149, 147, 121, 119, 111, 106, 98, 93, 75, 71, 71, 71, 69, 63, 61, 61, 56, 52, 52, 52, 48, 48, 48, 46, 46, 44, 44, 44, 44, 37, 37, 37, 36, 36, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 32, 22, 22, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 20, 20, 20, 21, 21, 21, 21, 19, 19, 17, 20, 16, 16, 25, 25, 25, 24, 25, 25, 27, 27, 27, 28, 27, 28, 28, 29, 33, \n35, 43, 45, 44, 44, 48, 56, 56, 58, 60, 77, 79, 79, 80, 82, 90, 88, 91, 21, 84, 92, 92, 92, 94, 95, 100, 101, 101, 101, 99, 101, 101, 102, 102, 104, 104, 104, 105, 109, 109, 112, 115, 115, 116, 117, 118, 122, 122, 122, 122, 125, 131, 132, 134, 141, 142, 142, 152, 157, 158, 164, 164, 173, 173, 177, 188, 188, 192, 192, 193, 196, 200, 202, 204, 203, 213, 214, 218, 226, 227, 227, 229, 226, 224, 224, 227, 220, 225, 236, 237, 246, 253, 256, 271, 298, 302, 313, 313, 317, 328, 324, 325, 316, 329, 329, 332, \n328, 320, 322, 321, 322, 307, 306, 311, 327, 317, 317, 322, 331, 333, 332, 332, 334, 341, 346, 347, 347, 348, 348, 354, 354, 360, 374, 378, 376, 377, 379, 379, 383, 391, 388, 388, 392, 392, 391, 395, 391, 395, 400, 402, 403, 411, 411, 409, 408, 416, 435, 446, 457, 459, 460, 461, 452, 453, 450, 439, 439, 435, 435, 434, 431, 427, 425, 421, 420, 410, 408, 404, 396, 395, 395, 393, 392, 391, 391, 388, 386, 381, 370, 369, 359, 352, 347, 332, 305, 300, 288, 287, 283, 271, 269, 267, 267, 254, 254, 251, 251, \n251, 248, 247, 245, 243, 241, 237, 223, 221, 221, 215, 206, 204, 204, 204, 201, 193, 187, 180, 180, 179, 179, 173, 173, 167, 152, 148, 148, 147, 145, 144, 136, 128, 128, 126, 122, 121, 121, 116, 116, 112, 107, 105, 101, 87, 86, 86, 80, 69, 53, 32, 16, 11, 4, 6, 16, 17, 20, 22, 22, 24, 24, 29, 36, 36, 38, 42, 45, 45, 45, 49, 49, 50, 57, 59, 59, 59, 60, 60, 60, 60, 60, 60, 61, 62, 63, 70, 70, 70, 70, 73, 73, 73, 73, 79, 83, 85, 86, 99, 99, 99, 100, 100, 101, 109, 109, 109, 113, 114, 119, 124, 128)
## uc009die.2 c(76, 76, 76, 76, 76, 86, 86, 90, 90, 91, 94, 97, 102, 103, 106, 109, 125, 126, 128, 128, 128, 128, 129, 132, 132, 132, 133, 133, 134, 136, 143, 143, 143, 144, 156, 156, 158, 159, 169, 169, 172, 172, 172, 172, 173, 173, 175, 175, 175, 175, 178, 183, 183, 186, 186, 189, 190, 191, 191, 191, 191, 191, 191, 191, 191, 192, 193, 193, 195, 195, 195, 195, 195)
## uc009dmb.2 c(11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 13, 14, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 21, 21, 18, 18, 18, 18, 18, 18, 18, 18, 20, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 25, 25, 25, 25, 27, 27, 27, 27, 28, 28, 28, 28, 29, 29, 29, 28, 28, 27, 27, 27, 27, 27, 27, 28, 28, 28, 26, 26, \n26, 26, 26, 26, 26, 24, 24, 24, 24, 22, 21, 18, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 15, 15, 13, 13, 13, 13, 12, 12, 12, 12, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 14, 13, 13, 13, 13, 13, 13, 19, 20, 20, 20, \n20, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 19, 17, 17, 17, 17, 17, 17, 18, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 23, 23, 23, 23, 23, 24, 23, 23, 23, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 27, 27, 27, 25, 25, 25, 25, 26, 25, 25, 25, 25, 25, 27, 27, 21, 20, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 22, 22)
## uc009eet.1 c(22, 22, 22, 22, 22, 21, 21, 21, 22, 22, 22, 22, 20, 20, 20, 19, 19, 19, 19, 19, 19, 21, 25, 25, 25, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 8, 8, 8, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 6, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, \n3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 6, 6, 6, 7, 9, 8, 8, 8, 8, 8, 8, 10, 10, 11, 16, 16, \n24, 24, 25, 26, 26, 27, 27, 26, 26, 26, 26, 30, 30, 30, 30, 30, 34, 34, 34, 40, 40, 40, 40, 41, 42, 42, 42, 42, 42, 42, 42, 42, 43, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 47, 48, 49, 49, 49, 49, 49, 49, 49, 49, 52, 52, 53, 53, 53, 53, 53, 53, 53, 57, 57, 57, 57, 55, 55, 54, 51, 52, 44, 44, 43, 42, 45, 44, 44, 44, 44, 44, 44, 40, 40, 41, 42, 42, 39, 39, 39, 36, 37, 38, 38, 37, 43, 43, \n43, 43, 43, 44, 44, 44, 43, 42, 42, 42, 42, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 53, 53, 57, 57, 57, 60, 60, 60, 62, 62, 62, 68, 68, 68, 68, 68, 70, 70, 70, 70, 70, 69, 68, 67, 67, 67, 68, 69, 69, 69, 69, 67, 67, 62, 62, 62, 61, 60, 60, 60, 56, 56, 56, 56, 56, 57, 57, 55, 54, 54, 55, 55, 55, 52, 52, 52, 52, 53, 53, 53, 56, 56, 55, 54, 54, 53, 55, 56, 53, 52, 51, 51, 51, 44, 45, 46, 46, 46, 48, 48, 48, 48, 48, 50, 51, 52, 47, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 49, 49, 44, \n46, 42, 42, 43, 42, 42, 42, 40, 40, 40, 35, 35, 35, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 35, 34, 34, 36, 36, 44, 44, 44, 44, 44, 44, 46, 47, 47, 48, 48, 50, 50, 50, 49, 49, 49, 50, 50, 49, 49, 49, 49, 49, 49, 49, 48, 48, 48, 45, 47, 48, 48, 48, 48, 46, 45, 48, 48, 48, 48, 48, 48, 47, 46, 48, 48, 46, 46, 46, 46, 48, 46, 45, 44, 44, 44, 44, 42, 42, 42, 42, 42, 42, 42, 42, 42, 39, 39, 39, 37, 37, 37, 36, 34, 37, 37, 37, 37, 37, 36, 36, 36, 33, 33, 33, 33, 33, 33, 34, 34, 35, 35, 35, 35, 35, \n33, 35, 33, 33, 24, 24, 24, 24, 24, 24, 23, 21, 21, 20, 20, 18, 18, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 21, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 14, 14, 14, 14, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 12, 12, 12, 12, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 16, 16, 16, 16, 15, 15, 16, 16, \n16, 17, 17, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 13, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 23, 23, 23, 23, 20, 20, 23, 24, 24, 24, 26, 26, 26, 26, 26, 25, 25, 25, 25, 26, 25, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 23, 24, 23, 23, 24, 23, 23, 23, 23, 23, 23, 23, 23, 23, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 25, 25, 25, 25, 28, \n28, 28, 28, 28, 28, 28, 31, 31, 32, 32, 32, 32, 32, 32, 31, 26, 24, 24, 24, 24, 34, 36, 39, 39, 39, 37, 38, 38, 38, 38, 39, 39, 39, 39, 44, 46, 46, 45, 45, 46, 46, 46, 46, 46, 46, 47, 48, 48, 48, 48, 48, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 52, 52, 52, 53, 51, 50, 54, 54, 53, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 57, 57, 57, 57, 57, 56, 57, 57, 57, 57, 57, 57, 57, 57, 54, 54, 54, 54, 54, 54, 54, 51, 51, 53, 58, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 49, 47, 46, 47, 47, 51, \n50, 50, 50, 53, 59, 60, 60, 57, 51, 52, 52, 51, 51, 50, 50, 50, 50, 50, 50, 53, 55, 58, 58, 58, 59, 58, 58, 58, 57, 57, 57, 57, 57, 57, 57, 57, 57, 61, 61, 62, 60, 60, 60, 59, 59, 59, 55, 55, 55, 52, 52, 52, 52, 52, 52, 53, 55, 56, 57, 56, 56, 57, 60, 60, 60, 59, 59, 59, 59, 62, 62, 62, 62, 66, 66, 66, 66, 66, 66, 66, 66, 66, 63, 58, 57, 57, 57, 57, 57, 57, 57, 62, 62, 63, 63, 63, 61, 62, 62, 57, 57, 58, 58, 56, 49, 48, 48, 49, 52, 49, 50, 50, 50, 51, 51, 51, 55, 55, 55, 51, 47, 45, 45, 45, 44, 44, \n45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 43, 43, 42, 43, 47, 50, 50, 50, 50, 50, 50, 51, 51, 51, 51, 51, 51, 51, 52, 50, 50, 47, 47, 47, 46, 43, 45, 45, 45, 45, 45, 45, 42, 42, 42, 42, 40, 41, 41, 41, 41, 41, 41)
## uc009eol.1 c(1408, 1412, 1384, 1385, 1398, 1399, 1385, 1408, 1416, 1460, 1513, 1544, 1569, 1623, 1677, 1685, 1700, 1712, 1717, 1726, 1738, 1742, 1754, 1734, 1727, 1685, 1695, 1699, 1709, 1689, 1671, 1728, 1732, 1719, 1727, 1724, 1739, 1744, 1743, 1766, 1756, 1787, 1779, 1819, 1839, 1980, 1995, 1998, 1995, 1990, 1958, 1942, 1928, 1922, 1919, 1930, 1910, 1907, 1895, 1885, 1885, 1886, 1886, 1896, 1884, 1870, 1863, 1825, 1846, 1842, 1825, 1797, 1675, 1668, 1659, 1659, 1657, 1655, 1645, 1635, 1617, 1595, 1577, 1579, \n1578, 1562, 1557, 1536, 1506, 1495, 1486, 1482, 1480, 1488, 1454, 1455, 1435, 1426, 1407, 1387, 1352, 1357, 1352, 1389, 1369, 1363, 1377, 1365, 1376, 1377, 1322, 1315, 1288, 1239, 1174, 1163, 1151, 1137, 1130, 1119, 1128, 1128, 1128, 1141, 1142, 1143, 1155, 1187, 1174, 1182, 1180, 1129, 1125, 1150, 1139, 1129, 1106, 1100, 1096, 1075, 1052, 1017, 992, 957, 942, 765, 755, 761, 765, 767, 769, 771, 776, 787, 788, 773, 772, 767, 760, 760, 756, 755, 753, 743, 743, 742, 740, 742, 710, 707, 699, 694, 689, \n689, 687, 684, 684, 679, 679, 664, 657, 657, 648, 634, 634, 633, 632, 631, 629, 629, 629, 628, 628, 614, 614, 603, 601, 601, 594, 590, 576, 561, 545, 502)
## Baf3_short.form.usage Baf3_long.form.usage Baf3_PDUI
## <numeric> <numeric> <numeric>
## uc009daz.2 29.6602572856635 283.389388104407 0.905253822444981
## uc009dhz.2 3.7254488495449 209.978806469604 0.982567268751943
## uc009die.2 121.8881378455 174.122891566265 0.588231093659866
## uc009dmb.2 9.22609762692124 9.11798839458414 0.497053294663731
## uc009eet.1 22.0449523788087 10.3274224192527 0.319019611124456
## uc009eol.1 1065.98013415893 221.456140350877 0.172013283092553
## short.mean long.mean PDUI P.Value
## <list> <list> <list> <list>
## uc009daz.2 29.6602572856635 283.389388104407 0.905253822444981 1
## uc009dhz.2 3.7254488495449 209.978806469604 0.982567268751943 1
## uc009die.2 121.8881378455 174.122891566265 0.588231093659866 1
## uc009dmb.2 9.22609762692124 9.11798839458414 0.497053294663731 1
## uc009eet.1 22.0449523788087 10.3274224192527 0.319019611124456 1
## uc009eol.1 1065.98013415893 221.456140350877 0.172013283092553 1
## adj.P.Val dPDUI PASS
## <list> <numeric> <logical>
## uc009daz.2 1 NaN FALSE
## uc009dhz.2 1 NaN FALSE
## uc009die.2 1 NaN FALSE
## uc009dmb.2 1 NaN FALSE
## uc009eet.1 1 NaN FALSE
## uc009eol.1 1 NaN FALSE
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengthssessionInfo()R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS
Matrix products: default BLAS: /home/biocbuild/bbs-3.10-bioc/R/lib/libRblas.so LAPACK: /home/biocbuild/bbs-3.10-bioc/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base
other attached packages:
[1] cleanUpdTSeq_1.24.0
[2] org.Hs.eg.db_3.10.0
[3] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[4] BSgenome.Mmusculus.UCSC.mm10_1.4.0
[5] BSgenome_1.54.0
[6] rtracklayer_1.46.0
[7] Biostrings_2.54.0
[8] XVector_0.26.0
[9] InPAS_1.18.0
[10] GenomicFeatures_1.38.0
[11] AnnotationDbi_1.48.0
[12] GenomicRanges_1.38.0
[13] GenomeInfoDb_1.22.0
[14] IRanges_2.20.0
[15] S4Vectors_0.24.0
[16] Biobase_2.46.0
[17] BiocGenerics_0.32.0
[18] BiocStyle_2.14.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 seqinr_3.6-1
[3] class_7.3-15 depmixS4_1.4-0
[5] biovizBase_1.34.0 htmlTable_1.13.2
[7] base64enc_0.1-3 dichromat_2.0-0
[9] rstudioapi_0.10 bit64_0.9-7
[11] splines_3.6.1 knitr_1.25
[13] zeallot_0.1.0 ade4_1.7-13
[15] Formula_1.2-3 Rsamtools_2.2.0
[17] cluster_2.1.0 dbplyr_1.4.2
[19] BiocManager_1.30.9 compiler_3.6.1
[21] httr_1.4.1 backports_1.1.5
[23] assertthat_0.2.1 Matrix_1.2-17
[25] lazyeval_0.2.2 limma_3.42.0
[27] acepack_1.4.1 htmltools_0.4.0
[29] prettyunits_1.0.2 tools_3.6.1
[31] gtable_0.3.0 glue_1.3.1
[33] GenomeInfoDbData_1.2.2 dplyr_0.8.3
[35] rappdirs_0.3.1 Rcpp_1.0.2
[37] vctrs_0.2.0 preprocessCore_1.48.0
[39] nlme_3.1-141 xfun_0.10
[41] stringr_1.4.0 ensembldb_2.10.0
[43] XML_3.98-1.20 zlibbioc_1.32.0
[45] MASS_7.3-51.4 scales_1.0.0
[47] VariantAnnotation_1.32.0 hms_0.5.1
[49] ProtGenerics_1.18.0 SummarizedExperiment_1.16.0
[51] AnnotationFilter_1.10.0 RColorBrewer_1.1-2
[53] yaml_2.2.0 curl_4.2
[55] memoise_1.1.0 gridExtra_2.3
[57] ggplot2_3.2.1 biomaRt_2.42.0
[59] rpart_4.1-15 latticeExtra_0.6-28
[61] stringi_1.4.3 RSQLite_2.1.2
[63] e1071_1.7-2 checkmate_1.9.4
[65] BiocParallel_1.20.0 truncnorm_1.0-8
[67] rlang_0.4.1 pkgconfig_2.0.3
[69] matrixStats_0.55.0 bitops_1.0-6
[71] Rsolnp_1.16 evaluate_0.14
[73] lattice_0.20-38 purrr_0.3.3
[75] GenomicAlignments_1.22.0 htmlwidgets_1.5.1
[77] bit_1.1-14 tidyselect_0.2.5
[79] magrittr_1.5 bookdown_0.14
[81] R6_2.4.0 Hmisc_4.2-0
[83] DelayedArray_0.12.0 DBI_1.0.0
[85] pillar_1.4.2 foreign_0.8-72
[87] BSgenome.Drerio.UCSC.danRer7_1.4.0 survival_2.44-1.1
[89] RCurl_1.95-4.12 nnet_7.3-12
[91] tibble_2.1.3 crayon_1.3.4
[93] BiocFileCache_1.10.0 rmarkdown_1.16
[95] progress_1.2.2 grid_3.6.1
[97] data.table_1.12.6 blob_1.2.0
[99] digest_0.6.22 openssl_1.4.1
[101] munsell_0.5.0 Gviz_1.30.0
[103] askpass_1.1
1. Sheppard, S., Lawson, N. D. & Zhu, L. J. Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naive bayes classifier. Bioinformatics 29, 2564–2571 (2013).