readBinFile: Read the bin-level text files containing ChIP and input...

In CSSP: ChIP-Seq Statistical Power

Description

Read the bin-level text files containing ChIP and input sample counts as well as M and GC scores.

Usage

readBinFile(type = c("chip", "input", "M", "GC"), fileName)

Arguments

type	A character vector indicating data types to be imported. This vector can contain "chip" (ChIP data), "input" (input data), "M" (mappability score), "GC" (GC content score). Default: c("chip","input","M","GC").
fileName	A character vector of file names, each of which matches each element of "type". "type" and "fileName". This vector should have the same length with "type" and corresponding elements in two vectors should appear in the same order.

Value

A data.frame of the processed bin files, containing ChIP, input, M and GC in different columns.

Note

"chip","input" and "M" files are all mandatory. "GC" file is optional.

Author(s)

Chandler [e-mail]

Examples

data( bindata.chr1 )
pwd <- getwd()
local({
setwd( tempdir() )
on.exit( setwd( pwd ) )
write.table( bindata.chr1[,c(1,4)], file = "chr1_map.txt", sep = "\t",
row.names = FALSE, col.names = FALSE )
write.table( bindata.chr1[,c(1,5)], file = "chr1_gc.txt", sep = "\t",
row.names = FALSE, col.names = FALSE )
write.table( bindata.chr1[,c(1,2)], file = "chr1_chip.txt", sep = "\t",
row.names = FALSE, col.names = FALSE )
write.table( bindata.chr1[,c(1,3)], file = "chr1_input.txt", sep = "\t",
row.names = FALSE, col.names = FALSE )
readBinFile( fileName = c("chr1_chip.txt", "chr1_input.txt", "chr1_map.txt",
"chr1_gc.txt" ) )
file.remove( paste( "chr1_", c( "chip", "input", "map", "gc" ), ".txt", sep = "" ) )
})

CSSP documentation built on Nov. 8, 2020, 8:26 p.m.