inferAlleles: inference of SNPs of ASEset

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

inference of SNPs

Usage

inferAlleles(
  x,
  strand = "*",
  return.type = "bi",
  threshold.frequency = 0,
  threshold.count.sample = 1,
  inferOver = "eachSample",
  allow.NA = FALSE
)

Arguments

x	ASEset
strand	strand to infer from
return.type	'uni' 'bi' 'tri' 'quad' 'all'
threshold.frequency	least fraction to classify (see details)
threshold.count.sample	least amount of counts to try to infer allele
inferOver	'eachSample' or 'allSamples'
allow.NA	treat NA as zero when TRUE

Details

threshold.frequency is the least fraction needed to classify as bi tri or quad allelic SNPs. If 'all' then all of bi tri and quad allelic SNPs will use the same threshold. Everything under the treshold will be regarded as noise. 'all' will return a matrix with snps as rows and uni bi tri and quad will be columns. For this function Anything that will return TRUE for tri-allelicwill also return TRUE for uni and bi-allelic for the same SNP an Sample.

Author(s)

Jesper R. Gadin

Examples

data(ASEset)
i <- inferAlleles(ASEset)

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