calc_candidate_regions: Determine candidate regions of selection

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Description

Determine candidate regions of selection.

Usage

calc_candidate_regions(
  scan,
  threshold = NA,
  pval = FALSE,
  ignore_sign = FALSE,
  window_size = 1e+06,
  overlap = 0,
  right = TRUE,
  min_n_mrk = 1,
  min_n_extr_mrk = 1,
  min_perc_extr_mrk = 0,
  join_neighbors = TRUE
)

Arguments

scan	a data frame containing scores (output of ihh2ihs, ines2rsb or ies2xpehh).
threshold	boundary score above which markers are defined as "extreme".
pval	logical. If TRUE use the (negative log-) p-value instead of the score.
ignore_sign	logical. If TRUE (default), take absolute values of score.
window_size	size of sliding windows. If set to 1, no windows are constructed and only the individual extremal markers are reported.
overlap	size of window overlap (default 0, i.e. no overlap).
right	logical, indicating if the windows should be closed on the right (and open on the left) or vice versa.
min_n_mrk	minimum number of markers per window.
min_n_extr_mrk	minimum number of markers with extreme value in a window.
min_perc_extr_mrk	minimum percentage of extremal markers among all markers.
join_neighbors	logical. If TRUE (default), merge neighboring windows with extreme values.

Details

There is no generally agreed method how to determine genomic regions which might have been under recent selection. Since selection tends to yield clusters of markers with outlier values, a common approach is to search for regions with an elevated number or fraction of outlier or extremal markers. This function allows to set three conditions a window must fulfill in order to classify as candidate region:

• min_n_mrk a minimum number of (any) markers.

• min_n_extr_mrk a minimum number of markers with outlier / extreme value.

• min_perc_extr_mrk a minimum percentage of extremal markers among all markers.

"Extreme" markers are defined by having a score above the specified threshold.

Value

A data frame with chromosomal regions, i.e. windows that fulfill the necessary conditions to qualify as candidate regions under selection. For each region the overall number of markers, their mean and maximum, the number of markers with extremal values, their percentage of all markers and their average are reported.

See Also

calc_region_stats

rehh documentation built on Sept. 15, 2021, 5:06 p.m.