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, chtaniguti@tamu.edu

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.

Examples

Run this code

# \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
# }

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