ODiogoSilva / vcf2PCA

Principal component analysis of SNP data with interactive plot

vcf2PCA

Principal component analysis of SNP data with the creation of an interactive plot

Requirements

vcf2PCA requires R and the following libraries:

• SNPRelate
• plotly

Installation

# SNPRelate
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")
install.packages("plotly")

Usage

vcf2PCA <vcf_file> <output_name> <pop_file (optional)>

The optional <pop_file> is a comma separated file with the name of the taxon in the first column and the corresponding group in the second column. Example:

TaxonA, Group1
TaxonB, Group1
TaxonC, Group2
.
.
.

Output example: