plotImpPCA: Plot PCAs 1-6

In sojwolf/ancientpca: A Probabilistic Approach to Conducting PCA with Sparse Genotype Data from Ancient Samples

Description

Exports plots of PCs 1~2, 3~4, 5~6 to PDF file

Usage

plotImpPCA(pca_obj, imputed_matrix, original_matrix, max_missing_snp = 1,
  max_missing_sample = 1, meta_file, output_pca_pdf)

Arguments

pca_obj	PCA object from R funtion prcomp()
imputed_matrix	Imputed genotype matrix with continuous genotype "probabilities"
original_matrix	Original genotype matrix coded 0,1,2, or <NA>
max_missing_snp	Set a max. percentage of missingness per SNP allowed. Default is set to 1 (i.e. 100 percent)
max_missing_sample	Set a max. percentage of missingness per sample allowed. Default is set to 1 (i.e. 100 percent)
meta_file	CVS file that contains headers "Sample_ID" and "Population". Can contain other columns as well.
output_pca_filename	Output file with ".pdf"

sojwolf/ancientpca documentation built on May 13, 2019, 9:53 p.m.