Nothing
select.snps <- function(x, condition) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
w <- eval(substitute(condition), x@snps, parent.frame())
miss <- is.na(w)
if(sum(miss)>0) {
warning(paste(sum(miss), 'SNP(s) with undefined condition are removed from bed.matrix'))
w <- w & !miss
}
x[,w]
}
select.inds <- function(x, condition) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
w <- eval(substitute(condition), x@ped, parent.frame())
miss <- is.na(w)
if(sum(miss)>0) {
warning(paste(sum(miss), 'individual(s) with undefined condition are removed from bed.matrix'))
w <- w & !miss
}
x[w,]
}
test.snps <- function(x, condition, na.to.false = TRUE) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
w <- eval(substitute(condition), x@snps, parent.frame())
miss <- is.na(w)
if(na.to.false & sum(miss)>0)
return(w & !miss)
w
}
test.inds <- function(x, condition, na.to.false = TRUE) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
w <- eval(substitute(condition), x@ped, parent.frame())
miss <- is.na(w)
if(sum(miss)>0)
return(w & !miss)
w
}
which.snps <- function(x, condition) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
which(eval(substitute(condition), x@snps, parent.frame()))
}
which.inds <- function(x, condition) {
if(!is(x, "bed.matrix")) stop("x is not a bed.matrix")
which(eval(substitute(condition), x@ped, parent.frame()))
}
is.autosome <- function(chr) chr %in% getOption("gaston.autosomes")
is.chr.x <- function(chr) chr %in% getOption("gaston.chr.x")
is.chr.y <- function(chr) chr %in% getOption("gaston.chr.y")
is.chr.mt <- function(chr) chr %in% getOption("gaston.chr.mt")
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