Description Usage Arguments Examples
View source: R/exported_functions.R
Identify closely-mapped repulsion-phase simplex x nulliplex markers and test these for preferential pairing, including estimating a preferential pairing parameter.
1 2 3 | test_prefpairing(dosage_matrix, maplist, LG_hom_stack, target_parent = "P1",
other_parent = "P2", ploidy = c(4, 6), min_cM = 0.5,
adj.method = "fdr", verbose = TRUE)
|
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. |
LG_hom_stack |
A |
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 |
verbose |
Should messages be send to stdout?
If |
1 2 | data("ALL_dosages","integrated.maplist","LGHomDf_P1_1")
P1pp <- test_prefpairing(ALL_dosages,integrated.maplist,LGHomDf_P1_1,ploidy=4)
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