clump.markers: Clump markers according to their LD.

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

Clump markers according to their LD.

Description

clumpMarkers implements clumping procedure (as described in PLINK documentation) on a gwaa.data-class object.

Usage

clump.markers(data, gwas.result, chr = 1, bp.dist = 250000, p1 = 1e-04,
  p2 = 0.01, r2 = 0.5, image = F, verbose = F)

Arguments

data	data object in gwaa.data-class,
gwas.result	gwaa.scan-class object with association test results,
chr	chromosome to be clumped,
bp.dist	threshold for inter-marker distance,
p1	threshold for index markers,
p2	threshold for clumping,
r2	threshold for LD,
image	a logical indicating whether to plot clumping results or not,
verbose	a logical indicating whether to print clumping results as it proceeds

Value

a list of clumps

Author(s)

Marcin Kierczak <[e-mail]>

References

http://pngu.mgh.harvard.edu/~purcell/plink/clump.shtml

Examples

## Not run: 
   clumps <- clump.markers(data.qc0, gwas.result = an0, chr = 6, bp.dist = 250e3, p1 = 0.0001, p2 = 0.01, r2 = 0.5, image=T)

## End(Not run)

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.