test_prefpairing {polymapR}

Check for and estimate preferential pairing

Description

Identify closely-mapped repulsion-phase simplex x nulliplex markers and test these for preferential pairing, including estimating a preferential pairing parameter.

Usage

test_prefpairing(
  dosage_matrix,
  maplist,
  LG_hom_stack,
  target_parent = "P1",
  other_parent = "P2",
  ploidy,
  min_cM = 0.5,
  adj.method = "fdr",
  verbose = TRUE
)

Arguments

dosage_matrix

An integer matrix with markers in rows and individuals in columns.

maplist

A list of integrated chromosomal maps, as generated by e.g. MDSMap_from_list. In the first column marker names and in the second their position.

LG_hom_stack

A data.frame with markernames ("SxN_Marker"), linkage group ("LG") and homologue ("homologue"), the output of define_LG_structure or bridgeHomologues usually.

target_parent

Character string specifying the parent to be tested for preferential pairing as provided in the columnnames of dosage_matrix, by default "P1".

other_parent

The other parent, by default "P2"

ploidy

The ploidy level of the species, by default 4 (tetraploid) is assumed.

min_cM

The smallest distance to be considered a true distance on the linkage map, by default distances less than 0.5 cM are considered essentially zero.

adj.method

Method to correct p values of Binomial test for multiple testing, by default the FDR correction is used, other options are available, inherited from p.adjust

verbose

Should messages be sent to stdout? If NULL log is send to stdout.

Examples

data("ALL_dosages","integrated.maplist","LGHomDf_P1_1")
P1pp <- test_prefpairing(ALL_dosages,integrated.maplist,LGHomDf_P1_1,ploidy=4)