R: Add a single marker to a map

add_marker {mappoly}

R Documentation

Add a single marker to a map

Description

Creates a new map by adding a marker in a given position in a pre-built map.

Usage

add_marker(
  input.map,
  mrk,
  pos,
  rf.matrix,
  genoprob = NULL,
  phase.config = "best",
  tol = 0.001,
  extend.tail = NULL,
  r.test = NULL,
  verbose = TRUE
)

Arguments

`input.map`	an object of class `mappoly.map`
`mrk`	the name of the marker to be inserted
`pos`	the name of the marker after which the new marker should be added. One also can inform the numeric position (between markers) were the new marker should be added. To insert a marker at the beginning of a map, use `pos = 0`
`rf.matrix`	an object of class `mappoly.rf.matrix` containing the recombination fractions and the number of homologues sharing alleles between pairwise markers on `input.map`. It is important that `shared.alleles = TRUE` in function `rf_list_to_matrix` when computing `rf.matrix`.
`genoprob`	an object of class `mappoly.genoprob` containing the genotype probabilities for all marker positions on `input.map`
`phase.config`	which phase configuration should be used. "best" (default) will choose the maximum likelihood configuration
`tol`	the desired accuracy (default = 10e-04)
`extend.tail`	the length of the chain's tail that should be used to calculate the likelihood of the map. If `NULL` (default), the function uses all markers positioned.
`r.test`	for internal use only
`verbose`	if `TRUE` (default), the current progress is shown; if `FALSE`, no output is produced

Details

add_marker splits the input map into two sub-maps to the left and the right of the given position. Using the genotype probabilities, it computes the log-likelihood of all possible linkage phases under a two-point threshold inherited from function rf_list_to_matrix.

Value

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, `chrom = NULL`
`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.ref = NULL`
`seq.alt`	alternative base used for each marker (i.e. A, T, C, G). If not available, `seq.ref = NULL`
`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 `mappoly.data`
`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 (`n.mrk - 1`) containing a sequence of recombination fraction between the adjacent markers in the map
`seq.ph`	linkage phase configuration for all markers in both parents
`loglike`	the hmm-based multipoint likelihood

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu

Examples


sub.map <- get_submap(maps.hexafake[[1]], 1:20, reestimate.rf = FALSE)
plot(sub.map, mrk.names = TRUE)
s <- make_seq_mappoly(hexafake, sub.map$info$mrk.names)
tpt <- est_pairwise_rf(s)
rf.matrix <- rf_list_to_matrix(input.twopt = tpt,
                               thresh.LOD.ph = 3, 
                               thresh.LOD.rf = 3,
                               shared.alleles = TRUE)
###### Removing marker "M_1" (first) #######
mrk.to.remove <- "M_1"
input.map <- drop_marker(sub.map, mrk.to.remove)
plot(input.map, mrk.names = TRUE)
## Computing conditional probabilities using the resulting map
genoprob <- calc_genoprob(input.map)
res.add.M_1 <- add_marker(input.map = input.map,
                        mrk = "M_1",
                        pos = 0,
                        rf.matrix = rf.matrix,
                        genoprob = genoprob,
                        tol = 10e-4)  
 plot(res.add.M_1, mrk.names = TRUE)                       
 best.phase <- res.add.M_1$maps[[1]]$seq.ph
 names.id <- names(best.phase$P)
 plot_compare_haplotypes(ploidy = 6,
                         hom.allele.p1 = best.phase$P[names.id],
                         hom.allele.q1 = best.phase$Q[names.id],
                         hom.allele.p2 = sub.map$maps[[1]]$seq.ph$P[names.id],
                         hom.allele.q2 = sub.map$maps[[1]]$seq.ph$Q[names.id])
                         
###### Removing marker "M_10" (middle or last) #######
mrk.to.remove <- "M_10"
input.map <- drop_marker(sub.map, mrk.to.remove)
plot(input.map, mrk.names = TRUE)
# Computing conditional probabilities using the resulting map
genoprob <- calc_genoprob(input.map)
res.add.M_10 <- add_marker(input.map = input.map,
                        mrk = "M_10",
                        pos = "M_9",
                        rf.matrix = rf.matrix,
                        genoprob = genoprob,
                        tol = 10e-4)  
 plot(res.add.M_10, mrk.names = TRUE)                       
 best.phase <- res.add.M_10$maps[[1]]$seq.ph
 names.id <- names(best.phase$P)
 plot_compare_haplotypes(ploidy = 6,
                         hom.allele.p1 = best.phase$P[names.id],
                         hom.allele.q1 = best.phase$Q[names.id],
                         hom.allele.p2 = sub.map$maps[[1]]$seq.ph$P[names.id],
                         hom.allele.q2 = sub.map$maps[[1]]$seq.ph$Q[names.id])

[Package mappoly version 0.4.1 Index]