onemap (version 3.0.0)

group_seq: Assign markers to preexisting linkage groups

Description

Identifies linkage groups of markers combining input sequences objects with unlinked markers from rf_2pts object. The results from two-point (pairwise) analysis and the transitive property of linkage are used for grouping, as group function.

Usage

group_seq(
  input.2pts,
  seqs = "CHROM",
  unlink.mks = "all",
  repeated = FALSE,
  LOD = NULL,
  max.rf = NULL,
  min_mks = NULL
)

Value

Returns an object of class group_seq, which is a list containing the following components:

data.name

name of the object of class onemap that contains the raw data.

twopt

name of the object of class rf.2ts used as input, i.e., containing information used to assign markers to linkage groups.

mk.names

marker names, according to the input file.

input.seqs

list with the numbers of the markers in each inputted sequence

input.unlink.mks

numbers of the unlinked markers in inputted sequence

out.seqs

list with the numbers of the markers in each outputted sequence

n.unlinked

number of markers that remained unlinked

n.repeated

number of markers which repeated in more than one group

n.mar

total number of markers evaluated

LOD

minimum LOD Score to declare linkage.

max.rf

maximum recombination fraction to declare linkage.

sequences

list of outputted sequences

repeated

list with the number of the markers that are repeated in each outputted sequence

unlinked

number of the markers which remained unlinked

Arguments

input.2pts

an object of class rf_2pts.

seqs

a list of objects of class sequence or the string "CHROM" if there is CHROM information available in the input data file.

unlink.mks

a object of class sequence with the number of the markers to be grouped with the preexisting sequences defined by seqs parameter. Using the string "all", all remaining markers of the rf_2pts object will be tested.

repeated

logical. If TRUE, markers grouped in more than one of the sequences are kept in the output sequences. If FALSE, they are removed of the output sequences.

LOD

a (positive) real number used as minimum LOD score (threshold) to declare linkage.

max.rf

a real number (usually smaller than 0.5) used as maximum recombination fraction to declare linkage.

min_mks

integer defining the minimum number of markers that a provided sequence (seqs or CHROM) should have to be considered a group.

Author

Cristiane Taniguti,

Details

If the arguments specifying thresholds used to group markers, i.e., minimum LOD Score and maximum recombination fraction, are NULL (default), the values used are those contained in object input.2pts. If not using NULL, the new values override the ones in object input.2pts.

See Also

make_seq and group

Examples

# \donttest{
data(onemap_example_out) # load OneMap's fake dataset for a outcrossing population
data(vcf_example_out) # load OneMap's fake dataset from a VCF file for a outcrossing population
comb_example <- combine_onemap(onemap_example_out, vcf_example_out) # Combine datasets
twopts <- rf_2pts(comb_example)

out_CHROM <- group_seq(twopts, seqs="CHROM", repeated=FALSE)
out_CHROM

seq1 <- make_seq(twopts, c(1,2,3,4,5,25,26))
seq2 <- make_seq(twopts, c(8,18))
seq3 <- make_seq(twopts, c(4,16,20,21,24,29))

out_seqs <- group_seq(twopts, seqs=list(seq1,seq2,seq3))
out_seqs
# }