getCountTable: getCountTable - obtaining typical count table.
In ampliQueso: Analysis of amplicon enrichment panels

Description Usage Arguments Value Author(s) Examples

Obtaining a count table for all the amplicons described in the BED file.

1	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

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library(ampliQueso)
setwd(path.package("ampliQueso"))
cc <- getCountTable(covdesc=system.file("extdata","covdesc",package="ampliQueso") , bedFile=system.file("extdata","AQ.bed",package="ampliQueso"))