mappoly (version 0.4.1)

add_marker: 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
)

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

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

Author

Marcelo Mollinari,

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.

Examples

# \donttest{
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]) 
# }