predict.haplogroup: Predict haplogroup (eg chrY or chrM), given labelled controls

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

Description

Predict haplogroup (eg chrY or chrM), given labelled controls

Usage

## S3 method for class 'haplogroup'
predict(gty, train, method = c("lda", "kmeans"),
  what = c("intensity", "genotypes"), noise = 0.1, ...)

Arguments

gty	a genotypes object with just the markers of interest
train	a genotypes object with labelled training samples

Details

We use linear discriminant analysis via (MASS::lda()) to extract the most informative dimensions of the input data, given the labelled training samples, and then project the test samples onto that dimension.

Value

a dataframe with predicted haplogroup membership for training samples; the result from the LDA procedure (see Details) is attached as attr(,"lda").

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