classifyCMS.SSP: classifyCMS.SSP

In Sage-Bionetworks/CMSclassifier: prediction of the Consensus Molecular Subtype (CMS) of colorectal carcinomas based on log2_scaled Gene Expression Profiles (GEP)

Description

nearest-centroid Single Sample Predictor (SSP) of the Consensus Molecular Subtype (CMS) of colorectal cancer samples, based on log2_scaled GEP

Usage

classifyCMS.SSP(Exp,minCor=.15,minDelta=.06)

Arguments

Exp	a dataframe with log2_scaled Gene Expression Profiles (GEP) data values, samples in columns, genes in rows, rownames corresponding to Entrez IDs
minCor	minimal correlation (sample x CMS centroid) for a sample to be classified in a CMS (NB : for a correlation below this threshold the sample will remain unclassified)
minDelta	minimal difference between the correlation of a sample to its two nearest centroids, to be classified in a CMS (NB: for a delta of correlation below this threshold the sample will remain unclassified)

Value

a dataframe, samples in rows, columns = correlation of the GEP to the four CMS centroids, nearest CMS, correlation to the nearest CMS, delta of correlation between the 2 nearest CMS, predicted CMS (NA value in case of uncertainty)

Note

This is a contribution from the Tumor Identity Cards (CIT) program founded by the 'Ligue Nationale Contre le Cancer' (France): http://cit.ligue-cancer.net. For any question please contact [e-mail]

Author(s)

Aurelien de Reynies

Sage-Bionetworks/CMSclassifier documentation built on May 9, 2019, 12:10 p.m.