make_it_012 {whoa}

just a quick function for making an 012 matrix from a character matrix

Description

The standard way within R of pulling values out of a named vector really bogs down on large data sets. So I will do this instead.

Usage

make_it_012(M)

Arguments

M

a character matrix of variant call format (VCF) genotypes and no dimnames. Allowable values are "0/0", and "0|0", which get coverted to integer 0; "0/1", "0|1", "1/0", and "1|0", which get converted to integer 1; and "1/1", and "1|1", which get converted to integer 2. Everything else gets converted to -1 to denote missing data.

Value

An integer matrix of values which are 0, 1, 2, or -1.

Examples

# get an 012 matrix from the lobster data
tmp <- t(vcfR::extract.gt(lobster_buz_2000, element = "GT"))
dimnames(tmp) <- NULL
g <- make_it_012(tmp)