getAlleleCounts: snp count data

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

Given the positions of known SNPs, this function returns allele counts from a BamGRL object

Usage

getAlleleCounts(BamList, ...)

## S4 method for signature 'GAlignmentsList'
getAlleleCounts(
  BamList,
  GRvariants,
  strand = "*",
  return.class = "list",
  verbose = TRUE,
  ...
)

Arguments

BamList	A GAlignmentsList object or GRangesList object containing data imported from a bam file
...	parameters to pass on
GRvariants	A GRanges object that contains positions of SNPs to retrieve
strand	A length 1 character with value '+', '-', or '*'. This argument determines if getAlleleCounts will retrieve counts from all reads, or only from reads marked as '+', '-' or '*' (unknown), respectively.
return.class	'list' or 'array'
verbose	Setting verbose=TRUE makes function more talkative

Details

This function is used to retrieve the allele counts from specified positions in a set of RNA-seq reads. The BamList argument will typically have been created using the impBamGAL function on bam-files. The GRvariants is either a GRanges with user-specified locations or else it is generated through scanning the same bam-files as in BamList for heterozygote locations (e.g. using scanForHeterozygotes). The GRvariants will currently only accept locations having width=1, corresponding to bi-allelic SNPs. In the strand argument, specifying '*' is the same as retrieving the sum count of '+' and '-' reads (and unknown strand reads in case these are found in the bam file). '*' is the default behaviour and can be used when the RNA-seq experiments strand information is not available.

Value

getAlleleCounts returns a list of several data.frame objects, each storing the count data for one SNP.

Author(s)

Jesper R. Gadin, Lasse Folkersen

See Also

• The scanForHeterozygotes which is a function to find possible heterozygote sites in a GenomicAlignments object

Examples

#load example data
data(reads)
data(GRvariants)


#get counts at the three positions specified in GRvariants
alleleCount <- getAlleleCounts(BamList=reads,GRvariants,
strand='*')

#if the reads had contained stranded data, these two calls would
#have given the correct input objects for getAlleleCounts
alleleCountPlus <- getAlleleCounts(BamList=reads,GRvariants,
strand='+')
alleleCountMinus <- getAlleleCounts(BamList=reads,GRvariants,
strand='-')

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.