qgg (version 1.0.4)

getW: Extract elements from genotype matrix (W) stored on disk

Description

Extract elements from genotype matrix W (whole or subset) stored on disk.

Usage

getW(
  Glist = NULL,
  bedfiles = NULL,
  ids = NULL,
  rsids = NULL,
  rws = NULL,
  cls = NULL,
  impute = TRUE,
  scale = FALSE,
  allele = NULL
)

Arguments

Glist

only provided if task="summary" or task="sparseld"

bedfiles

vector of name for the PLINK bed-file

ids

vector of ids in W to be extracted

rsids

vector of rsids in W to be extracted

rws

vector of rows in W to be extracted

cls

vector of columns in W to be extracted

impute

logical if TRUE missing genotypes are set to its expected value (2*af where af is allele frequency)

scale

logical if TRUE the genotype markers have been scale to mean zero and variance one

allele

vector of alleles to be extracted