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

In kulmsc/modLassosum: LASSO with summary statistics and a reference panel

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

Details

keep, remove could 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 have no headers. Likewise extract, exclude can also take one of the three formats, except with the role of the FID/IID data.frame replaced with a character vector of SNP ids (matching those in the .bim file).

Value

a list with

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

kulmsc/modLassosum documentation built on May 5, 2019, 9:19 a.m.