initialize-ASEset {AllelicImbalance} | R Documentation

## Initialize ASEset

### Description

Functions to construct ASEset objects

### Usage

    ASEsetFromCountList(rowRanges, countListUnknown = NULL,
      countListPlus = NULL, countListMinus = NULL, colData = NULL,
      mapBiasExpMean = NULL, phase = NULL, aquals = NULL, verbose = FALSE,
      ...)

    ASEsetFromArrays(rowRanges, countsUnknown = NULL, countsPlus = NULL,
      countsMinus = NULL, colData = NULL, mapBiasExpMean = NULL,
      phase = NULL, genotype = NULL, aquals = NULL, verbose = FALSE, ...)

### Arguments

`rowRanges` | A `GenomicRanges object` that contains the variants of interest
`countListUnknown` | A `list` where each entry is a matrix with allele counts as columns and sample counts as rows
`countListPlus` | A `list` where each entry is a matrix with allele counts as columns and sample counts as rows
`countListMinus` | A `list` where each entry is a matrix with allele counts as columns and sample counts as rows
`colData` | A `DataFrame` object containing sample specific data
`mapBiasExpMean` | A 3D `array` where the SNPs are in the 1st dimension, samples in the 2nd dimension and variants in the 3rd dimension.
`phase` | A `matrix` or an `array` containing phase information.
`aquals` | A 4-D array containing the countinformation, see details
`verbose` | Makes function more talkative
`...` | arguments passed on to SummarizedExperiment constructor
`countsUnknown` | An array containing the countinformation
`countsPlus` | An array containing the countinformation
`countsMinus` | An array containing the countinformation
`genotype` | matrix

### Details

The resulting ASEset object is based on the RangedSummarizedExperiment class, and will therefore inherit the same accessors and ranges operations.

If both countListPlus and countListMinus are given they will be used to calculate countListUnknown, which is the sum of the plus and minus strands.

countListPlus, countListMinus and countListUnknown are i.e. the outputs from the getAlleleCounts function.

aquals is new for the devel branch and will be changed slighly before the relase to include better granularity.

### Value

`ASEsetFromCountList` returns an `ASEset` object.

### Note

`ASEsetFromCountList` requires the same input data as a RangedSummarizedExperiment, but with minimum one assay for the allele counts.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    #make example alleleCountListPlus
    set.seed(42)
    countListPlus <- list()
    snps <- c('snp1','snp2','snp3','snp4','snp5')
    for(snp in snps){
    count<-matrix(rep(0,16),ncol=4,dimnames=list(
    c('sample1','sample2','sample3','sample4'),
    c('A','T','G','C')))
    #insert random counts in two of the alleles
    for(allele in sample(c('A','T','G','C'),2)){
    count[,allele]<-as.integer(rnorm(4,mean=50,sd=10))
    }
    countListPlus[[snp]] <- count
    }

    #make example alleleCountListMinus
    countListMinus <- list()
    snps <- c('snp1','snp2','snp3','snp4','snp5')
    for(snp in snps){
    count<-matrix(rep(0,16),ncol=4,dimnames=list(
    c('sample1','sample2','sample3','sample4'),
    c('A','T','G','C')))
    #insert random counts in two of the alleles
    for(allele in sample(c('A','T','G','C'),2)){
    count[,allele]<-as.integer(rnorm(4,mean=50,sd=10))
    }
    countListMinus[[snp]] <- count
    }

    #make example rowRanges
    rowRanges <- GRanges(
    seqnames = Rle(c('chr1', 'chr2', 'chr1', 'chr3', 'chr1')),
             ranges = IRanges(1:5, width = 1, names = head(letters,5)),
             snp = paste('snp',1:5,sep='')
             )
    #make example colData
    colData <- DataFrame(Treatment=c('ChIP', 'Input','Input','ChIP'),
     row.names=c('ind1','ind2','ind3','ind4'))

    #make ASEset
    a <- ASEsetFromCountList(rowRanges, countListPlus=countListPlus,
    countListMinus=countListMinus, colData=colData)

[Package AllelicImbalance version 1.18.0 Index]