readTabledBamGaps {spliceSites} | R Documentation |
readTabledBamGaps
readTabledBamGaps(infiles,idxInfiles=paste(infiles,".bai",sep=""),prof,rpmg=TRUE)
infiles |
character. Names of BAM-files. |
idxInfiles |
character. Names of BAM-index files. When given index file is not found, the function attempts to create a BAM-index file whith the depicted name. |
prof |
data.frame. Contains group affiliations for each BAM-file. Each column describes an entity by which values are grouped. The row-number in |
rpmg |
logical. When TRUE, there will be group specific rpmg align-rates be added to the result table |
The function reads gap-align data from all given BAM-files. For each factor level, the number of probes and aligns are counted. When gptm=TRUE
also the gptm values are written for each group. The result table contains for each prof factor level 2 (or 3) extra columns.
gapSites
Wolfgang Kaisers
bam<-character(2) bam[1]<-system.file("extdata","rna_fem.bam",package="spliceSites") bam[2]<-system.file("extdata","rna_mal.bam",package="spliceSites") prof<-data.frame(gender=c("f","m")) rtbg<-readTabledBamGaps(bam,prof=prof,rpmg=TRUE) rtbg getProfile(rtbg)