write.table_STARcounts: STAR counts

In gdmosher/STARcounts: Combine STAR Aligner Per Sample Read Counts to .xls File

Description

This function loads preexisting STAR Aligner count files *ReadsPerGene.out.tab$ from results_path, accumulates the data into a data frame, then writes the results in xls format to table_name.

Usage

write.table_STARcounts(
  results_path = "./results",
  table_name = "STARcountDFeByg.xls",
  dbg = 0
)

Arguments

results_path	Path to the STAR Aligner count files
table_name	Name of the output file including the .xls extension
dbg	Optional debug level defaults to 0

Details

_SampleName_.ReadsPerGene.out.tab must already exist (created during mapping step)
annotation.gtf must already exist before the mapping step, ./gffread -T annotation.gff -o annotation.gtf

Examples

results_path <- system.file("extdata", "results/", package = "STARcounts")
write.table_STARcounts(results_path=results_path, table_name="STARcountDFeByg.xls")
countDF <- read.delim("STARcountDFeByg.xls", row.names=1, check.names=FALSE)
head(countDF)

gdmosher/STARcounts documentation built on Jan. 7, 2020, 8:46 a.m.