processNDF: Reads in a Nimblegen microarray design file (NDF)

In markrobinsonuzh/Repitools: Epigenomic tools

Reads in a Nimblegen microarray design file (NDF)

Description

Reads a Nimblegen microarray design file (NDF file) which describes positions and sequences of probes on a Nimblegen microarray.

Usage

processNDF(filename = NULL, ncols = 768)

Arguments

filename	the name of the Nimblegen microarray design file
ncols	the number of columns of probes on the array - must be the same value as will be passed to loadPairFile or loadSampleDirectory. The default works for 385K format arrays.

Details

Reads in a Nimblegen microarray design file. This enables the reading in and annotation of Nimblegen microarray data files (pair files).

Value

a data frame containing

chr	the chromosome the probe was designed against
position	the position of the sequence the probe was designed against (probe centre)
strand	the strand the probe was designed against
index	the index (x y position) the probe occupies on the array
sequence	the actual DNA sequence synthesised onto the array
GC	the percent GC content of the probe sequence

Author(s)

Aaron Statham

See Also

loadSampleDirectory, loadPairFile

Examples

# Not run
#
## Read in the NDF file 
# ndfAll <- processNDF("080310_HG18_chr7RSFS_AS_ChIP.ndf")
#
## Subset the NDF to only probes against chromosomes
# ndf <- ndfAll[grep("^chr", ndfAll$chr),]

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.