replace.map: Swap out the marker map for a different one

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Swap out the marker map for a different one

Usage

replace.map(gty, newmap, ...)

Arguments

gty	a genotypes object
newmap	a valid marker map (especially: rownames same as marker names)
...	ignored

Details

Replacement of the marker map relies on marker names: only markers with which are shared by the old and new maps are retained in the output. (As such, this function is also a backdoor subsetting function.) Intensity matrices, BAF/LRR matrices, and site filters are adjusted accordingly. A validity check is performed before the function returns to flag problems.

Value

a copy of gty with old marker map replaced by the new one

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.