getCountTable {ampliQueso} | R Documentation

## getCountTable - obtaining typical count table.

### Description

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

### Usage

    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

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

[Package ampliQueso version 1.20.0 Index]