readBed: Read genotypes from PLINK bed file into R

In CollapsABEL: Generalized CDH (GCDH) Analysis

Description

Read genotypes from PLINK bed file into R

Usage

readBed(rbed_info, snp_vec, fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,ANY,logical,logical'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,missing,missing,missing'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,ANY,missing,missing'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,missing,logical,missing'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,ANY,logical,missing'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,missing,missing,logical'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,ANY,missing,logical'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

## S4 method for signature 'RbedInfoC,missing,logical,logical'
readBed(rbed_info, snp_vec,
  fid_iid = TRUE, snp_names_as_colnames = TRUE)

Arguments

rbed_info	RbedInfoC object
snp_vec	numeric. Vector of SNP index. Either row numbers in the bim file or a vector of SNP names.
fid_iid	logical. Whether the FID and IID columns should be included.
snp_names_as_colnames	logical. Whether SNP names should be used as colnames in the returned data frame

Value

data.frame Genotype data from bed file.

Author(s)

Kaiyin Zhong, Fan Liu

CollapsABEL documentation built on May 1, 2019, 7:28 p.m.