TickAtLab_pedigree: TickAtLab_pedigree

In moritzlindner/mousecolonytools: A collection of tools to facilitate genotyping and mouse colony management

TickAtLab_pedigree

Description

A convenience function for easily converting a TickAtLab table into a kinship2:pedigree.

Usage

TickAtLab_pedigree(
  df,
  defining.colnames = list(id = "Tier.ID1", dadid = "Vater", momid = "Mutter", sex =
    "G", status = "IsDead"),
  features = NULL
)

Arguments

df	A data.frame containing pedigree information. It should include columns for 'Tier.ID1', 'Vater', 'Mutter', 'G', and 'IsDead' by default. You can change the column names by specifying the 'defining.colnames' argument.
defining.colnames	A list specifying the column names for 'id', 'dadid', 'momid', 'sex', and 'status' in the input data.frame. The default values correspond to the most commonly used column names.
affected	additional column names from data frame or either of: "Task", short for "HasTask","HadTask"; "Tasks", short for "HasTask","HadTask","ParticipatesInActiveMating"; NULL, indicating affection status. All columns need to contain data convertible into logical

Details

The function ensures that the input data.frame is converted to the correct format expected by the kinship2 package. It checks and converts specific columns to the required data types ('id', 'dadid', 'momid' to character and 'status' to numeric). It also checks that the 'sex' column only contains the values 'm' (male) and/or 'f' (female).

Value

An object of class pedigree or pedigreeList Containing the following items: famid id findex mindex sex affected status relation @examples data(minnbreast) bpeds <- with(minnbreast, pedigree(id, fatherid, motherid, sex, affected=proband, famid=famid)) bped.id8 <- bpeds['8'] print(bped.id8) ## show this pedigree with mixed zygosity quadruplets rel8 <- data.frame(id1=c(137,138,139), id2=c(138,139,140), code=c(1,2,2)) bped.id8 <- with(minnbreast[minnbreast$famid==8,], pedigree(id, fatherid, motherid, sex, affected=proband, relation=rel8)) print(bped.id8)

Author(s)

Moritz Lindner

Examples

# Sample data.frame containing pedigree information
my_df <- data.frame(
  Tier.ID1 = c("Ind1", "Ind2", "Ind3"),
  Vater = c("V1", NA, "V1"),
  Mutter = c("M1", NA, "M2"),
  G = c("m", "f", "f"),
  IsDead = c(0, 1, 0)
)
# Convert data.frame to pedigree object
pedigree_obj <- TickAtLab_pedigree(df = my_df)

moritzlindner/mousecolonytools documentation built on Aug. 6, 2023, 6:45 a.m.