Tests | R Documentation |
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 |
A |
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
chr
, id
, dist
, pos
, A1
, A2
If basic stats have been computed (see set.stats
), N0
, N1
, N2
, NAs
, callrate
, maf
, hz
, etc.
If Hardy-Weinberg Equilibrium test has been performed (see set.hwe
), hwe
.
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))
.
select.snps
, select.inds
, set.stats
, set.hwe
# 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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