README.md

In scottwalmsley/THOR: Determines a spectral count threshold cutoff.

THOR

Cupoyright 2012 Scott Walmsley Testing for Heteroskedasticity of Sample Replicates : mass spectrometry count data cutoff MS data tool developed in R.

Requirements:

1. R
2. PeptideProphet MSMS search engine results.
3. ProteinProphet MSMS search engine results.
4. ABACUS results (see Damian Fermin's software at: http://abacustpp.sourceforge.net/).

Usage: Run from R command prompt:

#Source all your files.

# Read in an abacus file
file = "ABACUS_Results.tsv"
dset = read.THOR(file)


# Run the Goldfeld-QUandt test for heteroskedastistity
r = gq.THOR(dset,STEP=2,PLOT=T)

# Estimate the GQ mediated cutoff.
est.THOR(r)

scottwalmsley/THOR documentation built on May 10, 2019, 9:53 a.m.