Once you have downloaded this software, firstly copy it into linux computer and run gunzip command to expact this software. Then using chmod command to let software be executable. For example: chmod +x fillGenotype
The parameters of this software is as follows:
fillGenotype -w <window-size> -k <K-value> -p <punishing score> -r <percent-ratio> -i <input-fle> -o <output-file>
-w, --windowSize
define window size
-k, --K-value
define the number of neighbor
-p, --noequalPunish
define punishing score when two genotypes are not same. It must be integer.
-r, --percentRatio
define the ratio which the most genotype account for in all neighbor genotype
-i, --inputFile
the name of input file
-o, --outputFile
the name of output file
The example containing complete parameter:
fillGenotype -w 80 -k 5 -p -7 -r 0.7 -i example.input -o example.output
INPUTFILE FORMAT EXAMPLE
For input file, each row is a SNP site and each column is an inbreeding line (or called an accession). You can see the test file "example.input" for details. For example, in the line 1 of the file, "A" and "C" represents both alleles at the SNP site, and "-" means missing data.
|
