generateGDS1KGgenotypeFromSNPPileup: TODO This function append the genotype and the file related...

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

TODO This function append the genotype and the file related to the pileup

Description

TODO

Usage

generateGDS1KGgenotypeFromSNPPileup(
  PATHGENO,
  listSamples,
  listPos,
  offset,
  minCov = 10,
  minProb = 0.999,
  seqError = 0.001,
  pedStudy,
  batch,
  studyDF,
  PATHGDSSAMPLE = NULL
)

Arguments

PATHGENO	TODO a PATH to a directory with the a file for each samples with the genotype.
listSamples	a array with the sample to keep
listPos	a array
offset	a integer to adjust if the genome start at 0 or 1
minCov	a array with the sample to keep
minProb	a array with the sample to keep
seqError	a array with the sample to keep
batch	a integer corresponding
studyDF	a data.frame with at least the column study.id, study.desc and study.platform
PATHGDSSAMPLE	TODO a PATH to a directory where a gds specific to the samples with coverage info is keep
pedDF	a data.frame with the sample info. Must have the column sample.id, Name.ID, sex, pop.group, superPop and batch. The unique id of pedDF is Name.ID and the row.name is Name.ID too.

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", package="RAIDS")

## TODO
gds <- "Demo GDS TODO"

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