loadMappedReads: Load mapped reads
In CSAR: Statistical tools for the analysis of ChIP-seq data

Description Usage Arguments Value Author(s) References See Also Examples

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

1	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 `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)

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

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##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.

CSAR documentation built on Nov. 8, 2020, 6:50 p.m.