pedtools (version 1.1.0)

readPed: Read a pedigree from file

Description

Reads a text file in pedigree format, or something fairly close to it.

Usage

readPed(
  pedfile,
  colSep = "",
  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

colSep

A column separator character, passed on as the sep argument of read.table(). The default is to separate on <U+2018>white space<U+2019>, that is one or more spaces, tabs, newlines or carriage returns. (Note: the parameter sep is used to indicate allele separation in genotypes.)

header

A logical. If NA, the program will interpret the first line as a header line it contains both "id" and "sex" as part of some entries (ignoring case).

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. comment.char and quote.

Value

A ped object or a list of such.

Details

If there are no headers, and no column information is provided by the user, the program assumes the following column order:

• family ID (optional; guessed from the data)

• individual ID

• father's ID

• mother's ID

• sex

• marker data (remaining columns)

Examples

# NOT RUN {
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)

# }