loadMappedReads {CSAR} | R Documentation |
This function load the output file of a read mapping software (eg:SOAP)
loadMappedReads(file, format = "SOAP", header = FALSE)
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 |
header |
Logical value indicating if the first line of the file should be skipped (TRUE) or not (FALSE) |
data.frame structure that can be used by mappedReads2Nhits
Jose M Muino, jose.muino@wur.nl
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.
CSAR-package
##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.