Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

readPed

Read a pedigree from file

Description

Read a pedigree from file

Usage

readPed(
  pedfile,
  header = NA,
  famid_col = NA,
  id_col = NA,
  fid_col = NA,
  mid_col = NA,
  sex_col = NA,
  marker_col = NA,
  locusAttributes = NULL,
  missing = 0,
  sep = NULL,
  validate = TRUE,
  ...
)

Arguments

pedfile

A file name
header

A logical. If NA, the program will interpret the first line as a header line if the first entry contains "id" AND the word "sex" is an entry.
famid_col

Index of family ID column. If NA, the program looks for a column named "famid" (ignoring case).
id_col

Index of individual ID column. If NA, the program looks for a column named "id" (ignoring case).
fid_col

Index of father ID column. If NA, the program looks for a column named "fid" (ignoring case).
mid_col

Index of mother ID column. If NA, the program looks for a column named "mid" (ignoring case).
sex_col

Index of column with gender codes (0 = unknown; 1 = male; 2 = female). If NA, the program looks for a column named "sex" (ignoring case). If this is not found, genders of parents are deduced from the data, leaving the remaining as unknown.
marker_col

Index vector indicating columns with marker alleles. If NA, all columns to the right of all pedigree columns are used. If sep (see below) is non-NULL, each column is interpreted as a genotype column and split into separate alleles with strsplit(..., split = sep, fixed = TRUE).
locusAttributes

Passed on to setMarkers() (see explanation there).
missing

Passed on to setMarkers() (see explanation there).
sep

Passed on to setMarkers() (see explanation there).
validate

A logical indicating if the pedigree structure should be validated.
...

Further parameters passed on to read.table(), e.g. sep, comment.char and quote.

Value

A ped object or a list of such.

Examples

tf = tempfile()

### Write and read a trio
trio = data.frame(id = 1:3, fid = c(0,0,1), mid = c(0,0,2), sex = c(1,2,1))
write.table(trio, file = tf, row.names = FALSE)
readPed(tf)

# With marker data in one column
trio.marker = cbind(trio, M = c("1/1", "2/2", "1/2"))
write.table(trio.marker, file = tf, row.names = FALSE)
readPed(tf)

# With marker data in two allele columns
trio.marker2 = cbind(trio, M.1 = c(1,2,1), M.2 = c(1,2,2))
write.table(trio.marker2, file = tf, row.names = FALSE)
readPed(tf)

### Two singletons in the same file
singles = data.frame(id = c("S1", "S2"),
                     fid = c(0,0), mid = c(0,0), sex = c(2,1),
                     M = c("9/14.2", "9/9"))
write.table(singles, file = tf, row.names = FALSE)
readPed(tf)

### Two trios in the same file
trio2 = cbind(famid = rep(c("trio1", "trio2"), each = 3), rbind(trio, trio))

# Without column names
write.table(trio2, file = tf, row.names = FALSE)
readPed(tf)

# With column names
write.table(trio2, file = tf, col.names = FALSE, row.names = FALSE)
readPed(tf, famid = 1, id = 2, fid = 3, mid = 4, sex = 5)

# Cleanup
unlink(tf)
pedtools

Creating and Working with Pedigrees and Marker Data

v0.9.7
GPL-3
Authors
Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>)
Initial release

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.