merge_maps | R Documentation |
Estimates the linkage phase and recombination fraction between pre-built maps and creates a new map by merging them.
merge_maps( map.list, twopt, thres.twopt = 10, genoprob.list = NULL, thres.hmm = "best", tol = 1e-04 )
map.list |
a list of objects of class |
twopt |
an object of class |
thres.twopt |
the threshold used to determine if the linkage phases compared via two-point analysis should be considered for the search space reduction (default = 3) |
genoprob.list |
a list of objects of class |
thres.hmm |
the threshold used to determine which linkage phase configurations should be returned when merging two maps. If "best" (default), returns only the best linkage phase configuration. NOTE: if merging multiple maps, it always uses the "best" linkage phase configuration at each block insertion. |
tol |
the desired accuracy (default = 10e-04) |
merge_maps
uses two-point information, under a given LOD threshold, to reduce the
linkage phase search space. The remaining linkage phases are tested using the genotype
probabilities.
A list of class mappoly.map
with two elements:
i) info: a list containing information about the map, regardless of the linkage phase configuration:
ploidy |
the ploidy level |
n.mrk |
number of markers |
seq.num |
a vector containing the (ordered) indices of markers in the map, according to the input file |
mrk.names |
the names of markers in the map |
seq.dose.p1 |
a vector containing the dosage in parent 1 for all markers in the map |
seq.dose.p2 |
a vector containing the dosage in parent 2 for all markers in the map |
chrom |
a vector indicating the sequence (usually chromosome) each marker belongs
as informed in the input file. If not available,
|
genome.pos |
physical position (usually in megabase) of the markers into the sequence |
seq.ref |
reference base used for each marker (i.e. A, T, C, G). If not available,
|
seq.alt |
alternative base used for each marker (i.e. A, T, C, G). If not available,
|
chisq.pval |
a vector containing p-values of the chi-squared test of Mendelian segregation for all markers in the map |
data.name |
name of the dataset of class |
ph.thres |
the LOD threshold used to define the linkage phase configurations to test |
ii) a list of maps with possible linkage phase configuration. Each map in the list is also a list containing
seq.num |
a vector containing the (ordered) indices of markers in the map, according to the input file |
seq.rf |
a vector of size ( |
seq.ph |
linkage phase configuration for all markers in both parents |
loglike |
the hmm-based multipoint likelihood |
Marcelo Mollinari, mmollin@ncsu.edu
#### Tetraploid example ##### map1 <- get_submap(solcap.dose.map[[1]], 1:5) map2 <- get_submap(solcap.dose.map[[1]], 6:15) map3 <- get_submap(solcap.dose.map[[1]], 16:30) full.map <- get_submap(solcap.dose.map[[1]], 1:30) s <- make_seq_mappoly(tetra.solcap, full.map$maps[[1]]$seq.num) twopt <- est_pairwise_rf(input.seq = s) merged.maps <- merge_maps(map.list = list(map1, map2, map3), twopt = twopt, thres.twopt = 3) plot(merged.maps, mrk.names = TRUE) plot(full.map, mrk.names = TRUE) best.phase <- merged.maps$maps[[1]]$seq.ph names.id <- names(best.phase$P) compare_haplotypes(ploidy = 4, best.phase$P[names.id], full.map$maps[[1]]$seq.ph$P[names.id]) compare_haplotypes(ploidy = 4, best.phase$Q[names.id], full.map$maps[[1]]$seq.ph$Q[names.id])
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.