getSnps: Retrieve SNPs from local file or database with additional...

Description Usage Arguments Value See Also Examples

Description

Gets all SNPs within the specified region either from a mapfile or those available in the HapMap project. Gets all SNPs with position either from a mapfile or from the HapMap project.

Usage

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getSnpsByWin(chr, bp.start, bp.end, map = NULL, pop.id = 2)
getSnpsByRS(snps, map = NULL, pop.id = 2)

Arguments

chr

character(1). A single chromosome number, formatted as in the referred mapfile or HapMap database

bp.start

numeric(1). Start base position of the window (inclusive)

bp.end

numeric(1). End base position of the window (inclusive)

map

When

  • NULL, will use hapmap snps

  • character(1): fully qualified pathname, reads PLINK map file as in readMapfile.R

  • data frame: assumes PLINK map file in map3 column format ("CHR", "SNP", "BP")

pop.id

numeric(1). HapMap population ID for which the SNPs are retrieved (should not have an effect but is mandatory, 2 = CEU)

snps

character. A vector of rs IDs.

...

May be parameters used by a subfunction (e.g. for LD calculation, can specify ped- and map parameters for genotype retrieval, see documentation of the function 'getGenotypes')

Value

byWin: A vector of SNPs A vector of SNPs and columns "SNP", "CHR" and "BP"

See Also

getGenotypes

Examples

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map.filename <- system.file("extdata", "example.map.xz", package = "postgwas")
getSnpsByWin(chr = 3, bp.start = 9300000, bp.end = 9500000, map = map.filename)
getSnpsByRS(snps = c("rs13240", "rs8411"), map = map.filename)

merns/postgwas documentation built on May 22, 2017, 4:16 a.m.