as.bed.matrix: Creation of a bed.matrix
In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/bm_as_bm.r

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

1 2	as.bed.matrix(x, fam, bim)

`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)

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".

A bed.matrix condensing all three arguments.

Hervé Perdry and Claire Dandine-Roulland

bed.matrix-class

1
2
3

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

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