Evaluation of a condition on SNPS or individuals in a bed.matrix
Evaluate a condition and return logical vector or indices
test.snps(x, condition, na.to.false = TRUE)
test.inds(x, condition, na.to.false = TRUE)
which.snps(x, condition)
which.inds(x, condition)x |
|
condition |
Condition used to select SNPs |
na.to.false |
If |
The conditions can involve global variables and all variables defined
in the data frame x@snps, in particular for test.snps and which.snps
and for test.inds and which.inds
famid, id, father, mother, sex, pheno
If basic stats have been computed (see set.stats),
N0, N1, N2, NAs, callrate, etc.
test.snps and test.inds return a logical vector of length ncol(x) and nrow(x) respectively. which.snps(x, condition) is
equivalent to which(test.snps(x, condition)) and which.inds(x, condition) to which(test.inds(x, condition)).
# Load data data(LCT) x <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim) # SNPs and individuals with a callrate < 100% w <- test.snps(x, callrate < 1) table(w) which.snps(x, callrate < 1) which.inds(x, callrate < 1)
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