pcapred-package: pcapred: Produce PC Eigenvector Predictions From Plink Input...

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

Description

Given PCA loadings from flashpca, plink, fastpca, etc and your own data, perform some sanity checking and preoduce PC loadings for your own data, stored in a PLINK format bed file.

Details

This is the software for "pcapred", written by Daniel Lawson ([e-mail]) and supporting a paper by Aliya Sarmanova, Tim Morris and Daniel Lawson (to appear).

See https://github.com/danjlawson/pcapred for details.

Author(s)

Maintainer: Daniel Lawson [e-mail]

References

To follow

Examples

## Not run: 
library("pcapred")

mydata=pcapred.ref::onek_genomes_tiny() # Gets the file location of
  # the tiny bim/bed/fam data included in pcapred's data package, pcapred.ref

dat=readbed(mydata) # Read "your" data
dat=mergeref(dat) # Merge with the reference
                # (using the included standard reference of
                # 18 UK Biobank Pcs by default)
pred=predictpcs(dat)  # Predict the first 18 UK Biobank PCs
writepred("projected.eigenvals",dat,pred) # Write output in plink --covar format

## End(Not run)

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