sequoia (version 2.0.7)

PedPolish: Pedigree fix

Description

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

Usage

PedPolish(
  Ped,
  GenoNames = NULL,
  ZeroToNA = TRUE,
  NAToZero = FALSE,
  DropNonSNPd = TRUE,
  FillParents = FALSE
)

Arguments

Ped

dataframe where the first 3 columns are id, dam, sire

GenoNames

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 GenoNames

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.

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.