Added greedyMix support for VCF (closes #17)

R/greedyMix.R

@@ -1,15 +1,16 @@
 #' @title Clustering of individuals
 #' @param data data file
 #' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
+#' @param verbose if \code{TRUE}, prints extra output information
 #' @importFrom utils read.delim
 #' @export
-greedyMix <- function(data, format) {
+greedyMix <- function(data, format, verbose = TRUE) {
 	format <- tolower(format)
 	if (format == "fasta") {
 		out <- load_fasta(data)
 	} else if (format == "vcf") {
-		stop("VCF files not yet supported." )
 		# TODO #17: implement load_vcf()
+		out <- vcfR::read.vcfR(data, verbose = verbose)
 	} else if (format == "sam") {
 		stop("SAM files not yet supported." )
 		# TODO #18: implement load_sam()

inst/ext/vcf_example.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
+##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
+20	1291018	rs11449	G	A	.	PASS	.	GT	0/0	0/1
+20	2300608	rs84825	C	T	.	PASS	.	GT:GP	0/1:.	0/1:0.03,0.97,0
+20	2301308	rs84823	T	G	.	PASS	.	GT:PL	./.:.	1/1:10,5,0

tests/testthat/test-greedyMix.R

@@ -39,13 +39,19 @@ context("Opening files on greedyMix")
 
 df_fasta <- greedyMix(
 	data   = paste(path_inst, "FASTA_clustering_haploid.fasta", sep="/"),
-	format ="fasta"
+	format = "FASTA"
+)
+df_vcf <- greedyMix(
+	data    = paste(path_inst, "vcf_example.vcf", sep="/"),
+	format  = "VCF",
+	verbose = FALSE
 )
 # TODO #17: add example reading VCF
 # TODO #18: add example reading SAM
 # TODO #19: add example reading Genpop
 test_that("Files are imported correctly", {
 	expect_equal(dim(df_fasta), c(5, 99))
+	expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
 })
 
 context("Linkage")