correctParentSex: Sets sex for animals listed as either a sire or dam.

In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description

Part of Pedigree Curation

Usage

correctParentSex(id, sire, dam, sex, recordStatus, reportErrors = FALSE)

Arguments

id	character vector with unique identifier for an individual
sire	character vector with unique identifier for an individual's father (NA if unknown).
dam	character vector with unique identifier for an individual's mother (NA if unknown).
sex	factor with levels: "M", "F", "U". Sex specifier for an individual.
recordStatus	character vector with value of "added" or "original", which indicates whether an animal was added or an original animal.
reportErrors	logical value if TRUE will scan the entire file and make a list of all errors found. The errors will be returned in a list of list where each sublist is a type of error found.

Value

A factor with levels: "M", "F", "H", and "U" representing the sex codes for the ids provided

Examples

library(nprcgenekeepr)
pedOne <- data.frame(id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
                     sire = c(NA, "s0", "s4", NA, "s1", "s1", "s2", "s2"),
                     dam = c(NA, "d0", "d4", NA, "d1", "d2", "d2", "d2"),
                     sex = c("F", "F", "M", "F", "F", "F", "F", "M"),
                     recordStatus = rep("original", 8),
                     stringsAsFactors = FALSE)
pedTwo <- data.frame(id = c("s1", "d1", "s2", "d2", "o1", "o2", "o3", "o4"),
                     sire = c(NA, "s0", "s4", NA, "s1", "s1", "s2", "s2"),
                     dam = c("d0", "d0", "d4", NA, "d1", "d2", "d2", "d2"),
                     sex = c("M", "M", "M", "F", "F", "F", "F", "M"),
                     recordStatus = rep("original", 8),
                     stringsAsFactors = FALSE)
pedOneCorrected <- pedOne
pedOneCorrected$sex <- correctParentSex(pedOne$id, pedOne$sire, pedOne$dam,
                                        pedOne$sex, pedOne$recordStatus)
pedOne[pedOne$sex != pedOneCorrected$sex, ]
pedOneCorrected[pedOne$sex != pedOneCorrected$sex, ]

pedTwoCorrected <- pedTwo
pedTwoCorrected$sex <- correctParentSex(pedTwo$id, pedTwo$sire, pedTwo$dam,
                                        pedTwo$sex, pedOne$recordStatus)
pedTwo[pedTwo$sex != pedTwoCorrected$sex, ]
pedTwoCorrected[pedTwo$sex != pedTwoCorrected$sex, ]

rmsharp/nprcmanager documentation built on April 24, 2021, 3:13 p.m.