Nothing
read.vcf <- function(file, max.snps, get.info = FALSE, convert.chr = TRUE, verbose = getOption("gaston.verbose",TRUE)) {
xx <- NULL;
filename <- path.expand(file)
if(missing(max.snps)) max.snps = -1L;
L <- .Call("gg_read_vcf2", PACKAGE = "gaston", filename, max.snps, get.info)
snp <- data.frame(chr = L$chr, id = L$id, dist = 0, pos = L$pos , A1 = L$A1, A2 = L$A2,
quality = L$quality, filter = factor(L$filter), stringsAsFactors = FALSE)
if(get.info) snp$info <- L$info
if(convert.chr) {
chr <- as.integer(L$chr)
chr[L$chr == "X" | L$chr == "x"] <- getOption("gaston.chr.x")[1]
chr[L$chr == "Y" | L$chr == "y"] <- getOption("gaston.chr.y")[1]
chr[L$chr == "MT" | L$chr == "mt"] <- getOption("gaston.chr.mt")[1]
if(any(is.na(chr)))
warning("Some unknown chromosomes id's (try to set convert.chr = FALSE)")
snp$chr <- chr
}
ped <- data.frame(famid = L$samples, id = L$samples, father = 0, mother = 0, sex = 0, pheno = NA, stringsAsFactors = FALSE)
x <- new("bed.matrix", bed = L$bed, snps = snp, ped = ped,
p = NULL, mu = NULL, sigma = NULL, standardize_p = FALSE,
standardize_mu_sigma = FALSE )
if(getOption("gaston.auto.set.stats", TRUE)) x <- set.stats(x, verbose = verbose)
x
}
read.vcf.filtered <- function(file, positions, max.snps, get.info = FALSE, convert.chr = TRUE, verbose = getOption("gaston.verbose",TRUE)) {
xx <- NULL;
filename <- path.expand(file)
if(missing(max.snps)) max.snps = -1L;
L <- .Call("gg_read_vcf_filtered", PACKAGE = "gaston", filename, positions, max.snps, get.info)
snp <- data.frame(chr = L$chr, id = L$id, dist = 0, pos = L$pos , A1 = L$A1, A2 = L$A2,
quality = L$quality, filter = factor(L$filter), stringsAsFactors = FALSE)
if(get.info) snp$info <- L$info
if(convert.chr) {
chr <- as.integer(L$chr)
chr[L$chr == "X" | L$chr == "x"] <- getOption("gaston.chr.x")[1]
chr[L$chr == "Y" | L$chr == "y"] <- getOption("gaston.chr.y")[1]
chr[L$chr == "MT" | L$chr == "mt"] <- getOption("gaston.chr.mt")[1]
if(any(is.na(chr)))
warning("Some unknown chromosomes id's (try to set convert.chr = FALSE)")
snp$chr <- chr
}
ped <- data.frame(famid = L$samples, id = L$samples, father = 0, mother = 0, sex = 0, pheno = NA, stringsAsFactors = FALSE)
x <- new("bed.matrix", bed = L$bed, snps = snp, ped = ped,
p = NULL, mu = NULL, sigma = NULL, standardize_p = FALSE,
standardize_mu_sigma = FALSE )
if(getOption("gaston.auto.set.stats", TRUE)) x <- set.stats(x, verbose = verbose)
x
}
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