Sib-pair Command: read pedigree

ClassData Declaration command
Nameread pedigree|merlin
Arguments <pedigree file name> | inline [skip <lines_at_beginning>] [nopedid] [nosex]

Reads a GAS type pedigree file either from an external file, or inline following the command. The inline data is terminated by a line containing ";;;;". The skip keyword leads to the skipping past that number of lines at the beginning of the file.

The nopedid and nosex modifiers allow the pedigree file to be missing a pedigree ID column (in which case all records are taken to belong to a single kindred), or a sex column. In the latter case, sex is imputed in a mating-consistent fashion. Combining both allows reading the basic pedigree description "triple" (id, fa, mo) used by many other packages.

MERLIN type pedigree files are automatically correctly dealt with, so the merlin keyword is accepted just for completeness. Similarly, a PLINK .ped pedigree file is also read automatically -- read pedigree and read linkage differ only in their handling of zeroes for quantitative trait data.


read pedigree inline
# ped id fa mo sex m1 trait
1 1 x x m 1/1 12.0
1 2 x x f 1/2 10.0
1 3 1 2 f 1/2  8.5

See also:

read linkage read pre-Makeped pedigree file
read ppd read post-Makeped pedigree file
read cases read nonpedigree data file

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