getCountTable: getCountTable - obtaining typical count table.

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

1
getCountTable(covdesc="covdesc", bedFile="amplicons.bed")

Arguments

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 )

Value

Count table with the number of columns the same as number of samples and the number of rows the same as number of amplicons.

Author(s)

Alicja Szabelska, Marek Wiewiorka, Michal Okoniewski

Examples

1
2
3
library(ampliQueso)
setwd(path.package("ampliQueso"))
cc <- getCountTable(covdesc=system.file("extdata","covdesc",package="ampliQueso") , bedFile=system.file("extdata","AQ.bed",package="ampliQueso"))

ampliQueso documentation built on May 2, 2019, 12:45 a.m.