Get gene-level counts from TSS data

Source: R/AllGenerics.R, R/getGeneCounts.R

Get gene-level counts from TSS data

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

# S4 method for CapSet
getGeneCounts(CSobject, transcriptGRL,
  regionAroundTSS = 500, single_end = TRUE, 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
single_end	Logical, indicating whether reads are single end
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()
#> Checking de-multiplexed R1 reads
#> Checking de-multiplexed R2 reads
#> Checking mapped file
#> Checking de-duplicated file
 # get gene counts, counting reads around 500 bp of the TSS
 gcounts <- getGeneCounts(cs, dm6trans)