whippetTranscriptChangeSummary {GeneStructureTools} | R Documentation |
Compare open reading frames for whippet differentially spliced events
whippetTranscriptChangeSummary(whippetDataSet, gtf.all = NULL, BSgenome, eventTypes = "all", exons = NULL, transcripts = NULL, NMD = FALSE, exportGTF = NULL)
whippetDataSet |
whippetDataSet generated from |
gtf.all |
GRanges gtf annotation (can be used instead of specifying exons and transcripts) |
BSgenome |
BSGenome object containing the genome for the species analysed |
eventTypes |
which event type to filter for? default = "all" |
exons |
GRanges gtf annotation of exons |
transcripts |
GRanges gtf annotation of transcripts |
NMD |
Use NMD predictions? (Note: notNMD must be installed to use this feature) |
exportGTF |
file name to export alternative isoform GTFs (default=NULL) |
data.frame containing signficant whippet diff data and ORF change summaries
Beth Signal
Other whippet data processing: coordinates
,
diffSplicingResults
,
filterWhippetEvents
,
formatWhippetEvents
,
junctions
, readCounts
,
readWhippetDIFFfiles
,
readWhippetDataSet
,
readWhippetJNCfiles
,
readWhippetPSIfiles
whippetFiles <- system.file("extdata","whippet/", package = "GeneStructureTools") wds <- readWhippetDataSet(whippetFiles) wds <- filterWhippetEvents(wds) gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf", package = "GeneStructureTools")) g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 whippetTranscriptChangeSummary(wds, gtf.all=gtf,BSgenome = g)