getCountTable {ampliQueso} | R Documentation |
Obtaining a count table for all the amplicons described in the BED file.
getCountTable(covdesc="covdesc", bedFile="amplicons.bed")
covdesc |
Covdesc-like data frame - BAM files are read from row names. Similar to covdesc in simpleaffy and rnaSeqMap - tab delimited table of BAM files and groupings. This is the table of experimental design. |
bedFile |
BED file with same genomic coordinates as in BAMs (preferably standard hg19 ) |
Count table with the number of columns the same as number of samples and the number of rows the same as number of amplicons.
Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski
library(ampliQueso) setwd(path.package("ampliQueso")) cc <- getCountTable(covdesc=system.file("extdata","covdesc",package="ampliQueso") , bedFile=system.file("extdata","AQ.bed",package="ampliQueso"))