as.bed.matrix: Creation of a bed.matrix

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Description

Creates a bed.matrix using a numeric matrix and two data frame for ped / snps slots

Usage

 
as.bed.matrix(x, fam, bim)

Arguments

x	A numeric matrix
fam	(Optionnal) A data frame (the contents of a .fam file)
bim	(Optionnal) A data frame (the contents of a .bim file)

Details

The data frame fam should have columns named "famid", "id", "father", "mother", "sex" and "pheno". The data frame bim should have columns named "chr", "id", "dist", "pos", "A1" and "A2".

Value

A bed.matrix condensing all three arguments.

Author(s)

Herv<c3><a9> Perdry and Claire Dandine-Roulland

See Also

bed.matrix-class

Examples

data(AGT)
x <- as.bed.matrix(AGT.gen, AGT.fam, AGT.bim)
x

Example output

Loading required package: Rcpp
Loading required package: RcppParallel

Attaching package: 'RcppParallel'

The following object is masked from 'package:Rcpp':

    LdFlags

Gaston set number of threads to 1. Use RcppParallel::setThreadsOptions() to modify this.

Attaching package: 'gaston'

The following object is masked from 'package:stats':

    sigma

The following objects are masked from 'package:base':

    cbind, rbind

A bed.matrix with 503 individuals and 361 markers.
snps stats are set
ped stats are set

gaston documentation built on Jan. 31, 2018, 1:05 a.m.