Principal component analysis of SNP data with the creation of an interactive plot
vcf2PCA requires R and the following libraries:
- SNPRelate
- plotly
# SNPRelate
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")
install.packages("plotly")
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
.
.
.
