Compare two marker maps
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.
compare_maps(map1, map2)
map1 |
A list of numeric vectors; each vector gives marker positions for a single chromosome. |
map2 |
A second map, in the same format as |
A data frame containing
marker - marker name
chr_map1 - chromosome ID on map1
pos_map1 - position on map1
chr_map2 - chromosome ID on map2
pos_map2 - position on map2
# 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.