clump.markers: Clump markers according to their LD

Description Usage Arguments Value Author(s) References Examples

Description

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

Usage

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

Arguments

p1

threshold for index markers,

p2

threshold for clumping,

r2

threshold for LD,

bp.dist

threshold for inter-marker distance,

chr

chromosome to be clumped,

an

gwaa.scan-class objectwith association test results,

data

data object in gwaa.data-class,

image

a logical indicating whether to plot clumping results or not.

Value

a list of clumps

Author(s)

Marcin Kierczak <Marcin.Kierczak@slu.se>

References

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

Examples

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

cgmisc documentation built on May 2, 2019, 5:50 p.m.