ped
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Table of Contents
PED
PED
The “ped” file format refers to the widely-used format for linkage pedigree data and used as input for the program PLINK. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Program information
- Mac
- Windows
Data type handled
- diploid
- AFLP
- MICROSAT
- Standard
Input Files
- whitespace (spaces and or tabs) separated text file *.txt/*.dat
- first line:
NumIndivs
number of individuals - second line:
NumLoci
number of loci - third line:
Digits
number of digits used to denote a particular allele - fourth line:
Format
Lumped
(genotype at a single locus is given by a single number) orNonLumped
- next lines:
LocusNames
names of all loci separated by whitespace - next lines: genotype data
- first character: number of the individual (numbering must be serially)
- next characters: genotypes (all on same line or on different lines)
Lumped
format: two alleles are encoded as one number,Digits
specify how many digits are used to represent each locusNonLumped
format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated- Missing data:
Lumped
: encoded as0
,NonLumped
: encoded as-1
(each allele at the missing locus must have a-1
)
AFLP data
Lumped
format+
band is present-
band is absent0
missing data
- data types can be mixed
Example
Lumped
data file:
NumIndivs 2 NumLoci 6 Digits 1 Format Lumped LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH 1 11 11 11 0 11 32 2 21 11 21 11 11 12
NonLumped
data file:
NumIndivs 2 NumLoci 6 Digits 1 Format NonLumped LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH 1 123 143 -1 -1 144 144 120 122 157 158 144 144 2 135 135 134 140 144 144 120 122 161 161 144 144
- AFLP data file (4 Microsat loci, 5 AFLP loci):
NumIndivs 2 NumLoci 9 Digits 1 Format Lumped LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5 1 11 12 13 11 + + + - + 2 22 33 11 22 - - 0 - - 3 12 13 13 11 + - - - +
How to cite
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
ped.1307458091.txt.gz · Last modified: 2011/06/07 16:48 (external edit)