AllelicImbalance (version 1.10.2)

initialize-ASEset: 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

Value

ASEsetFromCountList returns an ASEset object.

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.

See Also

• RangedSummarizedExperiment objects.

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)