isoformSwitchAnalysisPart1 {IsoformSwitchAnalyzeR} | R Documentation |
This high-level function takes either a CuffSet object or a pre-existing switchAnalyzeRlist as input. If the input is a CuffSet object a switchAnalyzeRlist is created or else the function uses the provieded switchAnalyzeRlist. Then isoform switches are predicted (unless switchTestMethod='none'
) and ORF are predicted if not already annotated. Lastly the function extracts the nucleotide sequence and the ORF AA sequences of the isoforms involved in isoform switches. Thes sequences are both saved to external files and added to the switchAnalyzeRlist to enable external and internal sequence analysis respectively.
This function is meant to be used as part 1 of the isoform switch analysis workflow, which can be followed by the second step via isoformSwitchAnalysisPart2
.
isoformSwitchAnalysisPart1( switchAnalyzeRlist, alpha = 0.05, dIFcutoff = 0.1, switchTestMethod='DEXSeq', orfMethod = "longest", genomeObject, cds = NULL, pathToOutput = getwd(), outputSequences = TRUE, overwriteORF=FALSE, quiet=FALSE )
switchAnalyzeRlist |
A |
alpha |
The cutoff which the (calibrated) fdr correct p-values must be smaller than for calling significant switches. Defualit is 0.05. |
dIFcutoff |
The cutoff which the changes in (absolute) isoform usage must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%). |
switchTestMethod |
A sting indicating which statistical method should be used for testing differential isoform usage. The following options are avilable:
|
orfMethod |
A string indicating which of the 4 ORF identification methods should be used. The methods are:
Default is |
genomeObject |
A |
pathToOutput |
A path to the folder in which the plots should be made. Default is working directory ( getwd() ). |
cds |
A CDSSet object containing annoated coding regions, see ?CDSSet and ?getCDS for more information. Only necessary if \'orfType\' arguments is \'longestAnnotated\' or \'mostUpstreamAnnoated\'. |
overwriteORF |
A logical indicating whether to overwrite the ORF analysis already stored in the supplied switchAnalyzeRlist. Default is FALSE. |
outputSequences |
A logical indicating whether transcript nucleotide and amino acid sequences should be outputted to |
quiet |
A logical indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE |
This function performs the first part of a Isoform Analysis Workflow by
Remove non-expressed isoforms and single-isoform genes (see preFilter)
Predict isoform switches unless switchTestMethod
is set to 'none'.
If no ORFs are annotated the isoforms are analyzed for open reading frames (ORFs, see analyzeORF)
The isoform nucleotide and ORF amino acid sequences are extracted and saved to fasta files as well as added to the switchAnalyzeRlist enabling external sequence analysis with CPAT, Pfam and SignalP (see vignette for more info).
This function have two outputs. It returns a switchAnalyzeRlist
object where information about the isoform switch test, ORF prediction and nt and aa sequences have been added. Secondly (if outputSequences
is TRUE) the nucleotide and amino acid sequence of transcripts involved in switches are also save as fasta files enabling external sequence analysis.
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
preFilter
isoformSwitchTestDEXSeq
isoformSwitchTestDRIMSeq
analyzeORF
extractSequence
data("exampleSwitchList") exampleSwitchList library(BSgenome.Hsapiens.UCSC.hg19) exampleSwitchList <- isoformSwitchAnalysisPart1( switchAnalyzeRlist=exampleSwitchList, genomeObject = Hsapiens, dIFcutoff = 0.4, # Set high for short runtime in example data outputSequences = FALSE # keeps the function from outputting the fasta files from this example ) exampleSwitchList