PSMtab2SAM {proBAMr} | R Documentation |
Generate SAM files from confident peptide-spectrum-matches (PSMs).
PSMtab2SAM(passedPSM, XScolumn = "mvh", exon_anno, proteinseq, procodingseq, ...)
passedPSM |
a data frame of PSMs passed FDR. |
XScolumn |
specify the column which represents the matching score. |
exon_anno |
a dataframe of exon annotations. |
proteinseq |
a dataframe containing protein ids and protein sequences. |
procodingseq |
a data frame cotaining coding sequence for each protein. |
... |
additional arguments |
a dataframe containing
Xiaojing Wang
load(system.file("extdata/GENCODE", "exon_anno.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "proseq.RData", package="proBAMr")) load(system.file("extdata/GENCODE", "procodingseq.RData", package="proBAMr")) options(stringsAsFactors=FALSE) passedPSM <- read.table(system.file("extdata", "passedPSM.tab", package="proBAMr"), sep='\t', header=TRUE) SAM <- PSMtab2SAM(passedPSM, XScolumn='mvh', exon, proteinseq, procodingseq) write.table(SAM, file=paste(tempdir(), '/test.sam', sep=''), sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE)