parseselect: Parse the keep/remove/extract/exclude/chr options

In tshmak/lassosum: LASSO with summary statistics and a reference panel

Description

Parse the keep/remove/extract/exclude/chr options

Usage

parseselect(
  bfile,
  extract = NULL,
  exclude = NULL,
  keep = NULL,
  remove = NULL,
  chr = NULL,
  export = FALSE,
  order.important = FALSE
)

Arguments

bfile	plink file stem
extract	SNPs to extract
exclude	SNPs to exclude
keep	samples to keep
remove	samples to remove
chr	a vector of chromosomes
export	Logical. Whether to include the bim and/or fam data in the returned object.
order.important	Logical. Whether to strictly enforce that the order of extract and/or keep must match with bim or fam, respectively.

Details

keep and remove can take one of three formats:

1. A logical vector indicating which indivduals to keep/remove,

2. A data.frame with two columns giving the FID and IID of the indivdiuals to keep/remove (matching those in the .fam file), or

3. A character scalar giving the text file with the FID/IID.

Note that these files should not contain headers.

extract and exclude can be of format type (1) or (3) describe above, or a character vector of SNP ids (matching those in the .bim file).

Value

A list containing:

keep	Either NULL or a logical vector of which individuals to keep
extract	Either NULL or a logical vector of which SNPs to extract
N	Number of rows in the PLINK bfile
P	Number of columns in the PLINK bfile
n	Number of rows in the PLINK bfile after keep
p	Number of columns in the PLINK bfile after extract
bfile	File path to bfile stub
bimfile	File path to bim file
famfile	File path to fam file
bim	Either NULL or a data frame of bim data
fam	Either NULL or a data frame of fam data

tshmak/lassosum documentation built on Sept. 24, 2020, 9:41 a.m.