group_seq: Assign markers to preexisting linkage groups

In onemap: Construction of Genetic Maps in Experimental Crosses

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
)

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.

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.

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

Author(s)

Cristiane Taniguti, [e-mail]

See Also

make_seq and group

Examples

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

onemap documentation built on Nov. 26, 2022, 9:05 a.m.