add_marker: Add a single marker to a map

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

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, [e-mail]

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]) 

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.