Description Usage Arguments Value Author(s) References Examples
clumpMarkers
implements clumping procedure
described in PLINK documentation on a
gwaa.data-class
object.
1 2 | clump.markers(data, an, chr = 1, bp.dist = 250000,
p1 = 1e-04, p2 = 0.01, r2 = 0.5, image = F)
|
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 |
|
data |
data object in
|
image |
a logical indicating whether to plot clumping results or not. |
a list of clumps
Marcin Kierczak <Marcin.Kierczak@slu.se>
http://pngu.mgh.harvard.edu/~purcell/plink/clump.shtml
1 2 3 4 | ## 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)
|
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