PASEXP_IPA {APAlyzer} | R Documentation |
Map reads to IPA regions and calculte relative expression of aUTR and cUTR regions.
PASEXP_IPA(dfIPAraw, dfLEraw, flS, Strandtype="NONE", nts=1)
dfIPAraw |
a dataframe containing 8 colmuns for Intronic PASs: 'PASid', 'gene_symbol', 'Chrom', 'Strand', 'Pos', 'upstreamSS', 'downstreamSS'. 'upstreamSS' means closest 5'/3' splice site to IPA, 'downstreamSS' means closest 3' splice site |
dfLEraw |
a dataframe containing 5 colmuns for 3' least exon: 'gene_symbol', 'Chrom', 'Strand', 'LEstart', 'TES'. 'LEstart' means the start position of last 3' exon. |
flS |
bamfile lists containing the file and path of bam files |
Strandtype |
strand type of the bam file; "forward" is forwand sequencing, "invert" is reverse sequencing and "NONE" is non-strand specific, Default is "NONE". |
nts |
number of threads used for computing, parameter used by featureCounts, nthread option, Default is 1 |
The function PASEXP_IPA()
return a dataframe
containning reads count, RPKM and
relative expression of aUTR and cUTR for each gene
Ruijia Wang
## count reads mapped to IPA regions and ## calculte relative expression of aUTR and cUTR regions ## using forward sequencing library("TBX20BamSubset") library("Rsamtools") library("GenomicAlignments") flsall = getBamFileList() extpath = system.file("extdata", "mm9_REF.RData", package="APAlyzer") load(extpath) IPA_OUTraw=PASEXP_IPA(dfIPA, dfLE, flsall, Strandtype="forward", nts=1)