View source: R/snp_duplicated.r
SNP.duplicated | R Documentation |
Determines which SNPs are duplicates of previous SNPs and returns their indices.
SNP.duplicated(x, by = "chr:pos")
x |
A bed.matrix or a data.frame |
by |
The criterium used to determined if SNP is duplicated. |
When x
is a bed.matrix, the data.frame x@bed
will be used.
The columns that will be taken in consideration
Are id
, chr
, pos
, A1
, and A2
. Not all columns
are mandatory, depending on the value of by
.
The possible values for by
are "chr:pos"
, "chr:pos:alleles"
, "id"
,
"id:chr:pos"
and "id:chr:pos:alleles"
.
The default is by = "chr:pos"
, which means that two SNPs are considered as duplicated if they have
same chr
and pos
values.
Currently, when using a criterium involving alleles, this function does not consider the possibility of alleles swaps or reference strand flips.
An integer vector of indices of SNPs which are duplicates of previously seen SNPs.
SNP.match
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