ASEset-scanForHeterozygotes: scanForHeterozygotes

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

Identifies the positions of SNPs found in BamGR reads.

Usage

scanForHeterozygotes(BamList, ...)

## S4 method for signature 'GAlignmentsList'
scanForHeterozygotes(
  BamList,
  minimumReadsAtPos = 20,
  maximumMajorAlleleFrequency = 0.9,
  minimumMinorAlleleFrequency = 0.1,
  minimumBiAllelicFrequency = 0.9,
  verbose = TRUE,
  ...
)

Arguments

BamList	A GAlignmentsList object
...	argument to pass on
minimumReadsAtPos	minimum number of reads required to call a SNP at a given position
maximumMajorAlleleFrequency	maximum frequency allowed for the most common allele. Setting this parameter lower will minimise the SNP calls resulting from technical read errors, at the cost of missing loci with potential strong ASE
minimumMinorAlleleFrequency	minimum frequency allowed for the second most common allele. Setting this parameter higher will minimise the SNP calls resulting from technical read errors, at the cost of missing loci with potential strong ASE
minimumBiAllelicFrequency	minimum frequency allowed for the first and second most common allele. Setting a Lower value for this parameter will minimise the identification of loci with three or more alleles in one sample. This is useful if sequencing errors are suspected to be common.
verbose	logical indicating if process information should be displayed

Details

This function scans all reads stored in a GAlignmentsList for possible heterozygote positions. The user can balance the sensitivity of the search by modifying the minimumReadsAtPos, maximumMajorAlleleFrequency and minimumBiAllelicFrequency arguments.

Value

scanForHeterozygotes returns a GRanges object with the SNPs for the BamList object that was used as input.

Author(s)

Jesper R. Gadin, Lasse Folkersen

See Also

• The getAlleleCounts which is a function that count the number of reads overlapping a site.

Examples

data(reads)
s <- scanForHeterozygotes(reads,verbose=FALSE)

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