zooplot_prophbd: Plot proportion of the genome associated with different HBD...

In RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Plot proportion of the genome associated with different HBD classes

Description

Plot the mean percentage of the genome in different HBD classes or the inbreeding coefficient obtained by summing autozygosity associated with HBD classes with a rate lower or equal to a threshold (e.g., including all HBD classes with longer and more recent HBD segments than a selected threshold).

Usage

zooplot_prophbd(input, cols = NULL, style = "barplot", cumulative = FALSE)

Arguments

input	a named list with one or several zres objects obtained after running zoorun. The zres objects are the output of the zoorun function. For instance, putting list(name1 = zres1, name2 = zres2). The function will then use the names in the plot (in case several zres objects are used).
cols	a vector with the colors to be used for each population or zres object.
style	select "barplot", "lines" or "boxplot" for the graphic styles. Boxplot can be used with a single zres file or population.
cumulative	a logical indicating whether mean autozygosity is estimated per class (FALSE) or summed over all HBD class with a rate smaller than a value (these cumulated values are obtained for every rate defined in the model). By default, this value is FALSE. When FALSE, the percentages correspond to the mean individual genome-wide probabilities of belonging to each HBD-class or to the fraction of the genome in an autozygosity class. When TRUE, we obtain the mean probability of belonging to an HBD class with a rate smaller or equal than a threshold (here we use the pre-defined rates of the model as thresholds), averaged over the whole genome and all individuals. This corresponds to report mean genomic inbreeding coefficients estimated with respect to different base populations obtained by selecting different thresholds T that determine which HBD classes are considered in the estimation of the genomic inbreeding coefficient (setting the base population approximately 0.5 * T generations ago).

Value

The function plots either the average proportion of the genome associated with different HBD classes or the average genomic inbreeding coefficient estimated with respect to different base populations (from young to older).

RZooRoH documentation built on Oct. 27, 2023, 9:07 a.m.