readreference: Read the Reference Data for a PC projection

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

Description

Read in SNP weightings, eigenvalues and SNP info.

SNP info must be in <fileroot>.afreq.gz Weights are read according to mode and transpose flag.

Plink weights are in <fileroot>.eigenvec.var.gz/<fileroot>.eigenvec.tvar.gz flashpca weights are in <fileroot>.tload.gz/<fileroot>.tload.gz

Plink (Eigen) values are in <fileroot>.eigenval flashpca (Singular) values are in <fileroot>.val

Usage

readreference(
  fileroot,
  mode = "flashpca",
  transpose = FALSE,
  checkonly = FALSE,
  minfreq = 0.001,
  verbose = TRUE
)

Arguments

fileroot	fileset to read in
mode	Data mode; one of flashpca (default) or plink
transpose	Whether SNP weights are transposed (default FALSE)
checkonly	default FALSE. If TRUE, no file reading is done but the files are checked for existing
minfreq	(default 0.001) minimum allele frequency allowed in the normalisation phase, to prevent ultra-rare SNPs from being upweighted too much
verbose	default TRUE. Whether to output progress.

Value

An object of class "referencedata" which is a list containing:

• snpweights (if !checkonly) The matrix of snp weights, with SNPs as rows and PCs as columns

• snpstats (if !checkonly) The matrix of snp statistics, with SNPs as rows

• pcvals (if !checkonly) A vector of PC Eigenvalues (plink) or SVD Singular vectors (flashpca) as appropriate.

• mode As provided in the call.

• transpose As provided in the call

• minfreq As provided in the call

• pcvalsfile The file intended to be used for pcvals

• snpweightsfile The file intended to be used for snpweights

• snpstatsfile The file intended to be used for snpstats

Examples

## Not run: 
tfile=pcapred.ref::ukb_pcs_18()
ref=readreference(tfile)

## End(Not run)

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