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Last data update: 2014.03.03

R: TargetExperiment object constructor.

initialize

R Documentation

TargetExperiment object constructor.

Description

initialize creates the TargetExperiment object architecture for the specified bed and alingment BAM files. If 'scanBamP' and/or 'pileupP' parameters are not specified, default values of their constructors will be used.

Usage

## S4 method for signature 'TargetExperiment'
initialize(.Object, bedFile, bamFile, fastaFile,
    scanBamP = NULL, pileupP = NULL, feature = NULL, attribute = NULL,
    BPPARAM = bpparam())

Arguments

`.Object`	TargetExperiment class.
`bedFile`	Character indicating the bed file full path.
`bamFile`	Character indicating the alignment and index bam files full paths.
`fastaFile`	Character indicating the full path to the genome reference and index files.
`scanBamP`	ScanBamParam indicating the parameters for read the BAM file.
`pileupP`	PileupParam indicating the parameters for pileup building.
`feature`	Character indicating the name of the feature that will be explored (e.g 'amplicon', 'exon').
`attribute`	Character indicating the name of the attribute that will be explored. Should be 'coverage' or 'medianCounts'.
`BPPARAM`	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

TargetExperiment object.

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

Examples

## Defining bam file, bed file and fasta file names and paths
if (interactive()){
    bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC",
        mustWork=TRUE)
    bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC",
        mustWork=TRUE)
    fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
        mustWork=TRUE)

    ## Creating a TargetExperiment object

    ## Defining feature parameter
    feature<-"amplicon"
    ## Defining attribute parameter
    attribute<-"coverage"
    ##Calling the constructor
    ampliPanel<-TargetExperiment(bedFile, bamFile, fastaFile, 
        attribute=attribute, feature=feature)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(TarSeqQC)
Loading required package: GenomicRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

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

    compact

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

    desc

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

    rename

Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-initialize.Rd_%03d_medium.png", width=480, height=480)
> ### Name: initialize
> ### Title: TargetExperiment object constructor.
> ### Aliases: initialize initialize,TargetExperiment-method
> 
> ### ** Examples
> 
> ## Defining bam file, bed file and fasta file names and paths
> #if (interactive()){
>     bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC",
+         mustWork=TRUE)
>     bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC",
+         mustWork=TRUE)
>     fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
+         mustWork=TRUE)
> 
>     ## Creating a TargetExperiment object
> 
>     ## Defining feature parameter
>     feature<-"amplicon"
>     ## Defining attribute parameter
>     attribute<-"coverage"
>     ##Calling the constructor
>     ampliPanel<-TargetExperiment(bedFile, bamFile, fastaFile, 
+         attribute=attribute, feature=feature)
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>