sequoia: PedPolish – R documentation

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PedPolish

Fix Pedigree

Description

Ensure all parents & all genotyped individuals are included, remove duplicates, rename columns, and replace 0 by NA or v.v..

Usage

PedPolish(
  Pedigree,
  gID = NULL,
  ZeroToNA = TRUE,
  NAToZero = FALSE,
  DropNonSNPd = TRUE,
  FillParents = FALSE,
  NullOK = FALSE,
  LoopCheck = TRUE,
  StopIfInvalid = TRUE
)

Arguments

`Pedigree`	dataframe where the first 3 columns are id, dam, sire.
`gID`	character vector with ids of genotyped individuals (rownames of genotype matrix).
`ZeroToNA`	logical, replace 0's for missing values by NA's (defaults to `TRUE`).
`NAToZero`	logical, replace NA's for missing values by 0's. If `TRUE`, ZeroToNA is automatically set to `FALSE`.
`DropNonSNPd`	logical, remove any non-genotyped individuals (but keep non-genotyped parents), & sort pedigree in order of `gID`.
`FillParents`	logical, for individuals with only 1 parent assigned, set the other parent to a dummy (without assigning siblings or grandparents). Makes the pedigree compatible with R packages and software that requires individuals to have either 2 or 0 parents, such as `kinship`.
`NullOK`	logical, is it OK for Ped to be NULL? Then NULL will be returned.
`LoopCheck`	logical, check for invalid pedigree loops by calling `getGenerations`.
`StopIfInvalid`	if a pedigree loop is detected, stop with an error (TRUE, default).

Details

Recognized column names are any that contain:

dam: "dam", "mother", "mot", "mom", "mum", "mat"
sire: "sire", "father", "fat", "dad", "pat"

sequoia requires the column order id - dam - sire; columns 2 and 3 are swapped if necessary.

Examples

## Not run: 
# To get the output pedigree into kinship2 compatible format:
PedP <- sequoia::PedPolish(SeqOUT$Pedigree, DropNonSNPd=FALSE,
                           FillParents = TRUE)
PedP$Sex <- with(PedP, ifelse(id %in% dam, "female",  "male"))
# default to 'male' to avoid warning: "More than 25% of the gender values are
#  'unknown'"

Ped.fix <- with(PedP, kinship2::fixParents(id=id, dadid=sire, momid=dam,
                                           sex=Sex))
Ped.k <- with(Ped.fix, kinship2::pedigree(id, dadid, momid, sex, missid=0))

## End(Not run)

sequoia

Pedigree Inference from SNPs

v2.3.3

GPL-2

Authors

Jisca Huisman [aut, cre]

Initial release

2021-04-30