normalise: Normalise SNPs according to a reference frequency under a...

In danjlawson/pcapred: Produce PC Eigenvector Predictions From Plink Input Data And Loadings

Description

Normalise a SNP count matrix by an external reference frequency distribution by mean and standard deviation predicted under a binomial model.

Usage

normalise(rawdatmat, f, ploidy = 2, minfreq = NULL, meanimpute = FALSE)

Arguments

rawdatmat	A matrix of SNP counts of the alternative allele; of dimension N by L
f	A snp frequency vector of length L
ploidy	ploidy of the data (2=diploid) ; maximum that rawdatmat can take
minfreq	a thresholding for very raw SNPs in the reference, to prevent them from being over-weighted
meanimpute	(default FALSE) whether to mean impute missing data

Value

A matrix of size N by L which is rawdatmat zero meaned and with theoretical s.d. 1

danjlawson/pcapred documentation built on Oct. 7, 2021, 3:47 p.m.