merge.genotypes: Merge two 'genotypes' objects which share markers

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

Description

Merge two genotypes objects which share markers

Usage

## S3 method for class 'genotypes'
merge(x, y, check.alleles = FALSE, verbose = TRUE, ...)

Arguments

x	a genotypes object
y	another genotypes object
check.alleles	logical; if TRUE, attempt to verify compatibility of marker maps and fix allele or strand swaps
verbose	logical; if TRUE, show lots of detail about the merge process, especially allele/strand swaps
...	ignored

Details

Both input objects should have the same allele coding (character vs. numeric, relative vs. absolute) before merging. Sharing of markers is established by the presence of overlapping rownames in the genotype matrices of the input, but alleles are NOT checked. Marker names must match exactly if they are to appear in the output. Intensity matrices, if present, are merged and carried over to the output. They will be marked as normalized only if they are marked as such in both input objects. Vectors of site and sample filters will be present in the output only if they are present in both input objects, and have the expected names. A logical OR is applied to the site filters – ie. a site will be marked as TRUE (filtered) if it is filtered in either or both input datasets.

Value

a genotypes object containing all samples in x and y, at all markers shared by x and y

Warnings

Sample filters currently are *dropped* by the merge operation.

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