Rank animals by genetic value

Part of Genetic Value Analysis

Usage

rankSubjects(rpt)

Arguments

rpt

a named list of data.frames containing genetic value data for the population, as made by the report ordering step. The element names decide the designation: lowVal and noParentage as described above, and every other element (for example imports, lowMk and highGu) is “High Value”. The tiers separate out the animals that are imports, those with low mean kinship (a mean-kinship z-score at or below zScoreCutoff), those with high genome uniqueness (gu above guCutoff), and the remainder; see reportGV.

Value

A list of dataframes with value and ranking information added. Elements with no rows are returned unchanged.

Details

Adds a rank column to each data.frame in rpt: integers from 1 to the total number of ranked animals, running on from one tier to the next in the order of the list. Animals in the noParentage element get an NA rank. Adds a value column designating each animal "High Value", "Low Value" (the lowVal element) or "Undetermined" (the noParentage element).

References

Vinson, A. and Raboin, M.J. (2015) "A Practical Approach for Designing Breeding Groups to Maximize Genetic Diversity in a Large Colony of Captive Rhesus Macaques (Macaca mulatta)" Journal of the American Association for Laboratory Animal Science, 2015 Nov, Vol.54(6), pp.700-707.

Examples

library(nprcgenekeepr)
finalRpt <- nprcgenekeepr::finalRpt
rpt <- rankSubjects(nprcgenekeepr::finalRpt)
rpt[["highGu"]][1, "value"]
#> [1] "High Value"
rpt[["highGu"]][1, "rank"]
#> [1] 1
rpt[["lowMk"]][1, "value"]
#> [1] "High Value"
rpt[["lowMk"]][1, "rank"]
#> [1] 122
rpt[["lowVal"]][1, "value"]
#> [1] "Low Value"
rpt[["lowVal"]][1, "rank"]
#> [1] 190