validate.genotypes: Check the integrity of a 'genotypes' object

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

Description

Check the integrity of a genotypes object

Usage

## S3 method for class 'genotypes'
validate(gty, ...)

Arguments

gty	a genotypes object
...	ignored

Details

A valid genotypes object must have the following: a genotypes matrix with row and column names; a valid marker map (chr,marker,cM,pos) whose rownames match the rownames of the genotypes matrix; filter flags for sites and samples, with appropriate dimensions; and an indicator for allele coding.

If sample metadata is present, it must be a dataframe with at least a column 'iid' which is identical to its rownames. A column 'sex' is strongly encouraged but its absence will not cause validation to fail.

If intensity data is present, the x- and y-intensity matrices will be checked for dimensions and names in manner analogous to the checks on the genotypes matrix. If LRR and BAF have been computed, they will be checked also.

Value

Logical scalar indicating whether object passes or fails integrity checks.

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