compare_maps: Compare two marker maps

Description Usage Arguments Value Examples

View source: R/compare_maps.R

Description

Compare two marker maps, identifying markers that are only in one of the two maps, or that are in different orders on the two maps.

Usage

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compare_maps(map1, map2)

Arguments

map1

A list of numeric vectors; each vector gives marker positions for a single chromosome.

map2

A second map, in the same format as map1.

Value

A data frame containing

Examples

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# load some data
iron <- read_cross2( system.file("extdata", "iron.zip", package="qtl2") )
gmap <- iron$gmap
pmap <- iron$pmap

# omit a marker from each map
gmap[[7]] <- gmap[[7]][-3]
pmap[[8]] <- pmap[[8]][-7]
# swap order of a couple of markers on the physical map
names(pmap[[9]])[3:4] <- names(pmap[[9]])[4:3]
# move a marker to a different chromosome
pmap[[10]] <- c(pmap[[10]], pmap[[1]][2])[c(1,3,2)]
pmap[[1]] <- pmap[[1]][-2]

# compare these messed-up maps
compare_maps(gmap, pmap)

qtl2 documentation built on Oct. 18, 2021, 1:06 a.m.