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

In merns/postgwas: GWAS Post-Processing Utilities

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

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

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, 2019, 6:53 p.m.