meiosis_report {polyqtlR}

Generate a 'report' of predicted meiotic behaviour in an F1 population

Description

Function to extract the chromosome pairing predictions as estimated by estimate_IBD. Apart from producing an overview of the pairing during parental meiosis (including counts of multivalents, per linkage group per parent), the function also applies a simple chi-squared test to look for evidence of non-random pairing behaviour from the bivalent counts (deviations from a polysomic model)

Usage

meiosis_report(IBD_list, visualise = FALSE, precision = 2)

Arguments

IBD_list

List of IBD probabilities as estimated by estimate_IBD using method 'hmm', or externally (e.g. using TetraOrigin)

visualise

Logical, by default FALSE. If TRUE, a plot of the pairing results is produced per LG. In order to flag extreme deviations from the expected numbers (associated with polysomic inheritance, considered the Null hypothesis), barplots are coloured according to the level of significance of the X2 test. Plots showing red bars indicate extreme deviations from a polysomic pattern.

precision

To how many decimal places should summed probabilities per bivalent pairing be rounded? By default 2.

Value

The function returns a nested list, with one element per linkage group in the same order as the input IBD list. Per linkage group, a list is returned containing the following components:

P1_multivalents

The count of multivalents in parent 1 (only relevant if bivalent_decoding = FALSE during IBD calculation)

P2_multivalents

Similarly, the count of multivalents in parent 2

P1_pairing

The counts of each bivalent pairing predicted in parent 1, with an extra column Pr(X2) which gives the p-value of the X2 test of the off-diagonal terms in the matrix. In the case of a tetraploid, pairing A with B automatically implies C with D pairing, so the count table contains a lot of redundancy. The table should be read using both row and column names, so row A and column B corresponds to the count of individuals with A and B pairing (and hence C and D pairing). In a hexaploid, A-B pairing does not imply a particular pairing configuration in the remaining homologues. In this case, row A and column B is the count of individuals where A and B were predicted to have paired, summed over all three bivalent configurations with A and B paired (AB-CD-EF, AB-CE-DF, AB-CF,DE).

P2_pairing

Same as P1_pairing, except using parent 2

ploidy

The ploidy of parent 1

ploidy2

The ploidy of parent 2

Examples

data("IBD_4x")
mr.ls<-meiosis_report(IBD_list = IBD_4x)