classify: Classify

In d3b-center/medullo-classifier-package: Medulloblastoma Classifier

Classify

Description

Function to Classify samples into Medulloblastoma subtypes using transcriptomic data.

Usage

classify(exprs = NULL, medulloGeneSetsUp = NULL)

Arguments

exprs	matrix containing gene expression values. The row names contain HUGO/HGNC gene symbols and the column names contain the sample identifiers.
medulloGeneSetsUp	list of 4 containing the gene signature associated with each of the 4 molecular subtypes of Medulloblastoma.

Details

Classifier for predicting amongst the 4 molecular subtypes of Medulloblastoma, Sonic Hedgehog (SHH), WNT, Group 3, and Group 4 from RNA-Seq or microarray data.

The input is an expression matrix. The following types of data are allowed as inputs: (1) FPKM (2) TPM (3) quantile normalized data (4) microarray data.

The expected output of this function is a dataframe containing three columns: sample name, best.fit which is a character vector containing the predicted Medulloblastoma subtypes (i.e. 'WNT', 'SHH', 'Group3', 'Group4') and p.value which has the p-values associated with the predictions.

Author(s)

Pichai Raman

Komal S. Rathi

Sherjeel Arif

Examples

# Load example data containing expression matrix
data(exprs_109401)

# use classification function on expression matrix
prediction <- medulloPackage::classify(exprs_109401)

# View classifier output
head(prediction)

d3b-center/medullo-classifier-package documentation built on June 28, 2023, 8:16 p.m.