getTableSNV: TODO

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

TODO

Description

TODO

Usage

getTableSNV(
  gds,
  gdsSample,
  sampleCurrent,
  study.id,
  minCov = 10,
  minProb = 0.999,
  eProb = 0.001
)

Arguments

gds	an object of class SNPRelate::SNPGDSFileClass, a SNP GDS file.
gdsSample	an object of class gdsn.class (a GDS node), or gds.class (a GDS file) containing the information about one sample.
sampleCurrent	a character string corresponding to the sample identifier used in pruningSample function.
study.id	a character string corresponding to the study identifier used in pruningSample function.
minCov	a single positive integer representing the minimum coverage needed to retain TODO. Default: 10.
minProb	a single numeric between 0 and 1 representing TODO. Default: 0.999.
eProb	a single numeric between 0 and 1 representing the probability of sequencing error. Default: 0.001.

Value

a data.frame containing:

• cnt.tot a single integer representing the total coverage for the SNV.

• cnt.ref a single integer representing the coverage for the reference allele.

• cnt.alt a single integer representing the coverage for the alternative allele.

• snp.pos a single integer representing the SNV position.

• snp.chr a single integer representing the SNV chromosome.

• normal.geno a single numeric 3 indicating that the normal genotype is unknown. TODO

• snp.index The boolean FALSE indicating TODO

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

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