snipe: Run SNIPE Analysis
In dnusinow/snipeR: Software for Network Inference of Proteomics Experiments

Description Usage Arguments Value Author(s) See Also Examples

Run SNIPE analysis on a pair of data sets. Can split the calculation load amongst multiple cores on a single machine.

1	snipe(treatment, control, species, njobs = 1, nperms.per.job = 1000000, dbpath = "snipe_maps")

`treatment`	Path to the file containing the treatment data.
`control`	Path to the file containing the control data.
`species`	NCBI Taxon ID for the species the data applies to.
`njobs`	Number of jobs to divide the work in to.
`nperms.per.job`	Number of permutations per job to run.
`dbpath`	Pathway to databases including STRING and ID maps.

Returns a table containing the following fields: Ensembl Protein ID (from STRING), Official Gene Symbol, Protein Description, Observed Spectral Count in the treatment, Observed spectral count in the control, Observed Chi score, uncorrected p-value, and multiple test corrected p-value.

David Nusinow dnusinow@partners.org

download.missing.maps

1 2	data("Tooth_Proteins") ## Not run: snipe.out <- snipe(treatment = tooth_germ, control= oral_tissue, njobs = 5, nperms.per.job = 200000, species = 10090, dbpath = "~/nethome/data/snipe_maps")