estimateAllelicFraction: TODO

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

TODO

Description

TODO

Usage

estimateAllelicFraction(
  gds,
  gdsSample,
  sampleCurrent,
  study.id,
  chrInfo,
  studyType = "DNA",
  minCov = 10,
  minProb = 0.999,
  eProb = 0.001,
  cutOffLOH = -5,
  cutOffHomoScore = -3,
  wAR = 9
)

Arguments

gds	an object of class SNPRelate::SNPGDSFileClass, a SNP GDS file.
gdsSample	TODO
sampleCurrent	A string corresponding to the sample.id use in LDpruning
study.id	A string corresponding to the study use in LDpruning
chrInfo	a vector chrInfo[i] = length(Hsapiens[[paste0("chr", i)]]) Hsapiens library(BSgenome.Hsapiens.UCSC.hg38)
studyType	a string with value as DNA, ...
minCov	an integer default 10
minProb	an numeric betweeen 0 and 1
eProb	an numeric betweeen 0 and 1 probability of sequencing error
cutOffLOH	log of the score to be LOH default -5
cutOffHomoScore	TODO
wAR	size-1 of the window to compute an empty box

Value

The integer 0 when successful.

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo pedigree file is located in this package
data.dir <- system.file("extdata", "RAIDS")

## TODO

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.