SNP.match: SNP matching

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

SNP matching

Description

Returns a vector of the positions of (first) SNP matching of its first argument in its second.

Usage

 SNP.match(x, table, by = "chr:pos:alleles") 

Arguments

x	A bed.matrix or a data.frame
table	A bed.matrix or a data.frame
by	The criterium used to matchSNPs

Details

When x is a bed.matrix, the data.frame x@bed will be used; the same holds for table. The columns that will be taken in consideration are id, chr, pos, A1, and A2. Not all columns are mandatory (see below).

The matching criterium is specified by parameter by. There are 5 possible criteria : (i) matching by chromosome and position with by = "chr:pos", (ii) matching by chromosome, position, and alleles with by = "chr:pos:alleles", (iii) matching by id with by = "id", (iv) matching by id, chromosome and position with by = "id:chr:pos", and (v) matching by id, chromosome, position and alleles with by = "id:chr:pos:alleles".

For each SNP in x, the function looks for the position of the first matching SNP in table. If alleles are included in the matching criterium (ie if allele columns A1 and A2 are present in x), the function also checks for SNP matching with swapped alleles (a SNP A/C would match a SNP C/A), or with reference strand flipped (i.e. a SNP A/C would match a SNP T/G) or both (a SNP A/C would match a SNP G/T).

This function should prove useful for data set merging.

Value

A named list with one or three members, depending on whether alleles are included in the matching criterium.

index	An integer vector giving the position of first match in table, or NA if there is no match
swap	A logical vector indicating whether the match is with swapped alleles
flip	A logical vector indicating whether the match is with flipped strand

See Also

SNP.duplicated

gaston documentation built on Dec. 28, 2022, 1:30 a.m.