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

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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ampliQueso)
Loading required package: rnaSeqMap
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: knitr
Loading required package: rgl
Loading required package: ggplot2
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Loading required package: genefilter
Loading required package: statmod
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ampliQueso/getCountTable.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getCountTable
> ### Title: getCountTable - obtaining typical count table.
> ### Aliases: getCountTable
> 
> ### ** Examples
> 
> library(ampliQueso)
> setwd(path.package("ampliQueso"))
> cc <- getCountTable(covdesc=system.file("extdata","covdesc",package="ampliQueso") , bedFile=system.file("extdata","AQ.bed",package="ampliQueso"))
....................> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>