appendStudy2GDS1KG: Create a study at GDS including the reference (first study...

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

Create a study at GDS including the reference (first study add)

Description

TODO

Usage

appendStudy2GDS1KG(
  PATHGENO = file.path("data", "sampleGeno"),
  fileNamePED,
  fileNameGDS,
  batch = 1,
  studyDF,
  listSamples = NULL,
  PATHSAMPLEGDS = NULL
)

Arguments

PATHGENO	TODO a PATH to the directory genotype file of 1KG The directory sampleGeno must contain matFreqSNV.txt.bz2
fileNamePED	TODO
fileNameGDS	a character string representing the file name of the GDS study file that will be created. TODO
batch	TODO . Default: 1.
studyDF	TODO
listSamples	A vector of string corresponding to the sample.ids. If NULL all samples are selected. Default: NULL.
PATHSAMPLEGDS	TODO a PATH to a directory where a gds specific to the samples with coverage info is keep. Default: NULL.

Value

The function returns 0L 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
fileNamePED <- "TODO"

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