as.data.frame.linkdat: linkdat to data.frame conversion

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

linkdat to data.frame conversion

Description

Convert a linkdat object to data.frame for pretty printing.

Usage

## S3 method for class 'linkdat'
as.data.frame(
  x,
  ...,
  famid = F,
  markers = seq_len(x$nMark),
  alleles = NULL,
  missing = NULL,
  singleCol = FALSE,
  sep = ""
)

Arguments

x	a linkdat object.
...	further arguments (not used).
famid	a logical indicating if the family identifier should be included as the first column.
markers	a numeric indicating which markers should be included/printed.
alleles	a character containing allele names, e.g. alleles=c('A','B').
missing	the character (of length 1) used for missing alleles. Defaults to '0'.
singleCol	a logical: Should the two alleles for each marker be pasted into one column or kept in separate columns?
sep	a single character to be used as allele separator if singleCol=TRUE.

Details

This function is mainly intended for pretty-printing linkdat objects (for instance it is called by print.linkdat). For direct manipulation of the pedigree and/or marker matrices, it is better to use as.matrix.linkdat.

Value

A data.frame.

See Also

as.matrix.linkdat

Examples

x = linkdat(toyped)
x

# Printing x as above is equivalent to:
as.data.frame(x, sep = '/', missing = '-', singleCol = TRUE)

paramlink documentation built on April 15, 2022, 9:06 a.m.