Description Usage Arguments Details Value Author(s) See Also Examples

Combine multiple distance matrices into a single distance matrix providing an overall summary

1 | ```
combinedist(..., method = c("median", "mean"))
``` |

`...` |
Set of distance matrices, as calculated by |

`method` |
Indicates whether to summarize using the median or the mean. |

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.

A distance matrix, with class `"lineupdist"`

. The individual
IDs are in the row and column names.

Karl W Broman, [email protected]

`distee`

, `disteg`

,
`summary.lineupdist`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ```
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)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.