combinedist {lineup} | R Documentation |
Combine distance matrices into a single such
Description
Combine multiple distance matrices into a single distance matrix providing an overall summary
Usage
combinedist(..., method = c("median", "mean"))
Arguments
... |
Set of distance matrices, as calculated by |
method |
Indicates whether to summarize using the median or the mean. |
Details
The row and column names of the input distance matrices define the individual IDs.
If the input distance matrices all have an attribute "denom"
(for
denominator) and method="mean"
, we use a weighted mean, weighted by
the denominators. This could be used to calculate an overall proportion.
Value
A distance matrix, with class "lineupdist"
. The individual
IDs are in the row and column names.
Author(s)
Karl W Broman, broman@wisc.edu
See Also
distee()
, disteg()
,
summary.lineupdist()
Examples
library(qtl)
# load example data
data(f2cross, expr1, expr2, pmap, genepos)
# calculate QTL genotype probabilities
f2cross <- calc.genoprob(f2cross, step=1)
# find nearest pseudomarkers
pmark <- find.gene.pseudomarker(f2cross, pmap, genepos)
# line up individuals
id1 <- findCommonID(f2cross, expr1)
id2 <- findCommonID(f2cross, expr2)
# calculate LOD score for local eQTL
locallod1 <- calc.locallod(f2cross[,id1$first], expr1[id1$second,], pmark)
locallod2 <- calc.locallod(f2cross[,id2$first], expr2[id2$second,], pmark)
# take those with LOD > 25
expr1s <- expr1[,locallod1>25,drop=FALSE]
expr2s <- expr2[,locallod2>25,drop=FALSE]
# calculate distance between individuals
# (prop'n mismatches between obs and inferred eQTL geno)
d1 <- disteg(f2cross, expr1s, pmark)
d2 <- disteg(f2cross, expr2s, pmark)
# combine distances
d <- combinedist(d1, d2)
# summary of problem samples
summary(d)
[Package lineup version 0.44 Index]