qgg (version 1.1.1)

getG: Extract elements from genotype matrix stored on disk

Description

Extract elements from genotype matrix (rows/columns, ids/rsids) stored on disk.

Usage

getG(
  Glist = NULL,
  chr = NULL,
  bedfiles = NULL,
  bimfiles = NULL,
  famfiles = NULL,
  ids = NULL,
  rsids = NULL,
  rws = NULL,
  cls = NULL,
  impute = TRUE,
  scale = FALSE
)

Arguments

Glist

list structure with information about genotypes stored on disk

chr

chromosome for which W is to be extracted

bedfiles

vector of name for the PLINK bed-file

bimfiles

vector of name for the PLINK bim-file

famfiles

vector of name for the PLINK fam-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