getGeneCounts: Get gene-level counts from TSS data

In icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Get gene-level counts from TSS data

Usage

getGeneCounts(
  CSobject,
  transcriptGRL,
  regionAroundTSS = 500,
  outfile = NA,
  ncores = 1
)

## S4 method for signature 'CapSet'
getGeneCounts(
  CSobject,
  transcriptGRL,
  regionAroundTSS = 500,
  outfile = NA,
  ncores = 1
)

Arguments

CSobject	The CapSet object to use.
transcriptGRL	A GRangesList object containing transcripts, created using transcriptsBy(txdb)
regionAroundTSS	integer, indicating how many bases downstream of TSS to count
outfile	character. Tab-separated output file name (if required)
ncores	integer. No. of cores/threads to use

Value

data.frame with gene-level counts for all genes in the txdb object

Examples

 # load a txdb object
 library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
 seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"

 # get transcripts by gene (only X chromsome, for simplicity)
 seqlevels(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "X"
 dm6trans <- transcriptsBy(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "gene")

 # load a CapSet object
 cs <- exampleCSobject()
 # get gene counts, counting reads around 500 bp of the TSS
 gcounts <- getGeneCounts(cs, dm6trans)

icetea documentation built on Nov. 8, 2020, 6:57 p.m.