`getSignificantSNPs` <-
function (x, chromosome, model, sig = 1e-15)
{
if (!inherits(x, "WGassociation"))
stop("x must be an object of class 'WGassociation'")
if(is.null(attr(x, "gen.info")))
{
pvalues <- attr(x, "pvalues")
mm<-charmatch(model,dimnames(pvalues)[[2]])
if (is.na(mm))
stop("model selected is not correct")
sel2<-pvalues[,mm]<=sig
SNPs.sel <- pvalues[sel2, ]
pos.sel <- attr(x, "colSNPs")[sel2]
out <- list(names = dimnames(SNPs.sel)[[1]], column = pos.sel)
}
else
{
if (!chromosome %in% c(1:22) & chromosome != "X")
stop("chromosome should be either a number between 1 and 22 or X")
if (chromosome == "X")
chromosome <- 23
gen.info <- attr(x, "gen.info")
pvalues <- attr(x, "pvalues")
chrs <- gen.info[, 2]
chr.l <- unique(chrs)
chr <- chr.l[orderChromosome(chr.l)]
sel <- chr[chromosome]
SNPs <- gen.info[gen.info[, 2] %in% sel, 1]
sel2 <- dimnames(pvalues)[[1]] %in% SNPs & !is.na(pvalues[,
2]) & pvalues[, 2] <= sig
SNPs.sel <- pvalues[sel2, ]
pos.sel <- attr(x, "colSNPs")[sel2]
out <- list(names = dimnames(SNPs.sel)[[1]], column = pos.sel)
}
out
}
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