2.1 Command Line Arguments
you can use help for usage:
perl SMAP.pl -h
Command line:
perl SMAP.pl -vf variant_peptide_table.txt[file] -g genotype.vcf[file] -o result.txt[file]
--variant_peptide,-vf (A file containing quantitative values of variant peptides; required)
--genotype, -g (A genotype file used sample verification; required )
--output, -o (An output filename; required)
--plex, -p (Multiplex number of the isobaric labeling approach)
--fold_change, -fc (Signal to Noise ratio (optional; default is 3))
--noise_level, -nl (The upper threshold of a noise level)
--version, -h (Print version)
--help, -h (Print help)
--licence, -l (Print licence)
2.2 Demo and Program Testing
If you download the standalone program under the folder of /home/User/Software/SMAP, you can test the program using the following command:
perl src/SMAP.pl -g data/genotype_table.vcf -vf data/variant_peptide_table.txt -o output.txt -fc 5
The program takes two inputs:
2.2.1 Variant peptide quantification table. The table contains peptide id, gene/protein name, peptide spectrum match(PSM), SNP id and the quantification data for each sample.
2.2.2 Genotype file in VCF format.
