calcScore: Calc score

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

Calc score

Description

Function to calculate the gene ratio for each sample.

Usage

calcScore(myMat = NULL, mySetsUp = NULL)

Arguments

myMat	matrix containing gene ratios for each gene signature and sample. The row names contain the gene signatures and the column names contain the individual samples.
mySetsUp	list of 4 containing the gene ratios associated with each of the 4 molecular subtypes of Medulloblastoma. Provided in the data directory as 'medulloSetsUp'.

Details

This function takes 2 input parameters. The first parameter is a gene ratio matrix in which the entries are the expression values for each gene signature. The second parameter is a list of 4, where each list has the gene ratios associated with the 4 Medulloblastoma subtypes.

The function takes the gene ratio matrix and computes the column mean. However, function does not use all the values in the column. Only the values of the gene ratios associated with a given Medulloblastoma subtype are used to compute a column mean.

The expected output is a list of two dataframes: one is a data frame where the rownames are the Sample Identifiers and the column names are the 4 Medulloblastoma subtypes. and the second is a data frame of t-test pvalues across all combination of subtypes per samples

Author(s)

Pichai Raman

Komal S. Rathi

Sherjeel Arif

Examples

## load provided data
data(geneRatioOut_109401)

## Use calcScore function
myMat <- calcScore(geneRatioOut_109401)

## View contents of matrix

# mean scores
head(myMat[[1]])

# t-test pvalues
head(myMat[[2]])

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