CSAR (version 1.24.0)

loadMappedReads: Load mapped reads

Description

This function load the output file of a read mapping software (eg:SOAP)

Usage

loadMappedReads(file, format = "SOAP", header = FALSE)

Arguments

file

File name to load

format

Format of the file. "SOAP" for the output of the soap software and "MAQ" for the maq software. Other user formats can be provided as a character vector for the file column names. Columns named: "Nhits", "lengthRead", "strand", "chr", and "pos" are needed.

header

Logical value indicating if the first line of the file should be skipped (TRUE) or not (FALSE)

Value

data.frame structure that can be used by mappedReads2Nhits

References

Muino et al. (submitted). Plant ChIP-seq Analyzer: An R package for the statistcal detection of protein-bound genomic regions. Kaufmann et al.(2009).Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biology; 7(4):e1000090.

See Also

CSAR-package

Examples

##We load the mapped reads:
#sample<-loadMappedReads(file=file,format="SOAP",w=300,header=F)
##where file is the name and path of the output file of the mapping process.