| op {purgeR} | R Documentation |
Opportunity of purging
Description
The potential reduction in individual inbreeding load can be estimated by means of the opportunity of purging (O) and expressed opportunity of purging (Oe) parameters described by Gulisija and Crow (2007). Whereas O relates to the total potential reduction of the inbreeding load in an individual, as a consequence of it having inbred ancestors, Oe relates to the expressed potential reduction of the inbreeding load. In both cases, these measures are referred to fully recessive, high effect size alleles (e.g. lethals). For complex pedigrees, involving more than one autozygous individual per path from a reference individual to an ancestor, these estimates are estimated following an heuristic approach (see details below).
Usage
op(ped, pi, Fi, name_O, name_Oe, sufix, compute_O = FALSE)
Arguments
ped |
A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns. |
pi |
Partial inbreeding matrix |
Fi |
Vector of inbreeding coefficient values |
name_O |
A string naming the new output column for total opportunity of purging (defaults to "O") |
name_Oe |
A string naming the new output column for the expressed opportunity of purging (defaults to "Oe") |
sufix |
A string naming the sufix for non-corrected O and Oe measures |
compute_O |
Enable computation of total opportunity of purging (false by default) |
Details
In simple pedigrees, the opportunity of purging (O) and the expressed opportunity of purging (Oe) are estimated as in Gulisija and Crow (2007). For complex pedigrees involving more than one autozygous individual per path from an individual to an ancestor, O and Oe in the closer ancestors need to be discounted for what was already accounted for in their predecessors. To solve this problem, Gulisija and Crow (2007) provide expression to correct O and Oe (see equations 21 and 22 in the manuscript).
Here, an heuristic approach is used to prevent the inflation of O and Oe,
and avoid the use of additional looped expressions that may result in an
excessive computational cost. To do so, when using ip_op(complex = TRUE)
only the contribution of the most recent ancestors in a path will be considered.
This may not provide exact values of O and Oe, but we expect little bias, since
more distant ancestors also contribute lesser to O and Oe.
Value
The input dataframe, plus two additional column named "O" and "Oe", containing total and expressed opportunity of purging measures.
References
Gulisija D, Crow JF. 2007. Inferring purging from pedigree data. Evolution 61(5): 1043-1051.