FilterPlinkSample: Making PLINK files with desired samples.

This function prepares PLINK binary files with the desired samples.

Usage

FilterPlinkSample(
  DataDir,
  ResultDir,
  finput,
  foutput = NULL,
  filter_sample = "cases",
  keep_remove_sample_file = NULL,
  keep = TRUE
)

Arguments

DataDir

Character string for the file path of the all input files.

ResultDir

character string for the file path where the output PLINK files will be stored.

finput

Character string, specifying the prefix of the input PLINK binary files.

foutput

Character string, specifying the prefix of the output PLINK binary files.

filter_sample

Character string, specifying the sample type to be retained. The choices are, "cases", "controls", "males" and "females". The default is "cases".

keep_remove_sample_file

Character string, specifying the prefix of a space/tab-delimited text file with no header. For the samples that we want to keep or remove, the family IDs should be in the first column and within-family IDs in the second column. This file needs to be in the DataDir. The default is NULL.

keep

Boolean value, TRUE or FALSE for specifying desired samples to keep or remove. The default is TRUE.

Value

NULL

The output PLINK files with passed samples will be saved in ResultDir.

Author

Banabithi Bose

Examples

DataDir <- GXwasR:::GXwasR_data()
ResultDir <- tempdir()
finput <- "GXwasR_example"
foutput <- "casesPlink"
filter_sample <- "cases"
keep_remove_sample_file <- "samples_example"
keep <- FALSE

FilterPlinkSample(
    DataDir = DataDir, ResultDir = ResultDir,
    finput = finput, foutput = foutput, keep_remove_sample_file = keep_remove_sample_file,
    keep = keep
)
#> ✔ casesPlink PLINK files with desired samples are in /var/folders/d6/gtwl3_017sj4pp14fbfcbqjh0000gp/T//RtmpO7c0S8
#> NULL