3 Using PseudoCons
The program PseudoCons takes a PLINK binary pedigree file as input and outputs a PLINK binary pedigree file:
./pseudocons -i mydata.bed -o pseudoData.bed
This requires that the corresponding .bim and .fam, files are also available. A text PLINK pedigree file, .ped, with corresponding map file, .map, may be used to create a binary file using PLINK as follows:
plink --noweb --file mydata --make-bed --out mydata
This will create the binary pedigree file, mydata.bed, map file, mydata.bim, and family file, mydata.fam required for use with PseudoCons.
If for some reason you should wish to have a text PLINK pedigree file, this can be created using PLINK as follows:
plink --noweb --bfile pseudoData --make-bed --out pseudoData --recode
This will create the text PLINK pedigree file pseudoData.ped with map file pseudoData.map.
Typing pseudocons with no options will output usage details:
PseudoCons: pseudocontrols from pedigree data v1.12
---------------------------------------------------
Copyright 2013-2014 Richard Howey, GNU General Public License, v3
Institute of Genetic Medicine, Newcastle University
Usage:
./pseudocons [options] inputFile
or ./pseudocons -pf parameterfile
Options:
-i filename -- input filename
-o filename -- output filename
-pc1 -- one pseudocontrol per trio
-pc3 -- three pseudocontrols per trio
-pc15 -- 15 pseudocontrols per trio (2 SNP interaction only)
-snpnos snp1 snp2 -- SNP numbers of pair to create 15 pseudocontrols per trio
-snpnames snp1 snp2 -- as above using SNP names
-cepg -- use CEPG giving 3, 7 and 31 pseudos for -pc1, 3 and 15
-info info.dat -- output info file
-info-fa info.dat -- output info file with father+child genotypes
-info-ma info.dat -- output info file with mother+child genotypes
-info-fama info.dat -- output info file with father+mother+child genotypes
-info-maxsnps n -- max number of SNPs allowed in info file (default=20)
-pro -- proband filename
-xtrio -- allow extra trios
-log -- log filename
-so -- suppress output to screen
Default options:
-pc1
A parameter file, .pf, may be used with PseudoCons instead of writing all of the options on the command line. To use a parameter file simply type:
./pseudocons myparameters.pf
The parameter file should be a text file with one option written on each line. For example, to perform the analysis above the file myparameters.pf would be as follows:
-i mydata.bed
-o myCasePseudoControlData.bed
-log myLog.log
-so
It is also possible to add comments to the file provided that the “-” character is not used, and to comment out any options by placing another character in front of any “-”. For example, the above parameter file could be edited as follows to perform the next analysis given above:
This is in input file from my really great study
-i mydata.bed
This will be my case/pseudocontrol data file
-o myCasePseudoControlData.bed
Keep a log of the PseudoCons output here
-log myLog.log
Suppress the output from the screen
-so
The following file types are input into PseudoCons:
| File | Description |
|---|
| .bed | binary PLINK file |
| .bim | extended map file with allele names |
| .fam | family pedigree PLINK file |
The following file types are output from PseudoCons:
| File | Description |
|---|
| .bed | binary PLINK file |
| .bim | extended map file with allele names |
| .fam | family pedigree PLINK file |
| .log | log file of PseudoCons |
If the -info info.dat option is used then an additional information file is output, see section 4.6.
