receptLoss: Identify genes with expression loss

Description Usage Arguments Value Examples

View source: R/scripts.R

Description

This function allows you to identify genes with loss of expression

Usage

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receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup)

Arguments

exprMatrNml

A matrix of expression values from normal tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrTum.

exprMatrTum

A matrix of expression values from tumor tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrNml.

nSdBelow

The number of SD below the mean of the adjacent normal tissue to set the boundary between tumor subgroups.

minPropPerGroup

A value between 0-1 that represents the minimum proportion of samples that should be present in each of the two subgroups (defined by the boundary set by nSdBelow) for a particular gene.

Value

a nx7 matrix, with n equaling the number of genes. The columns are as follows:

Examples

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exprMatrNml <- matrix(abs(rnorm(100, mean=2)), nrow=10)
exprMatrTum <- matrix(abs(rnorm(100)), nrow=10)
geneNames <- paste0(letters[seq_len(nrow(exprMatrNml))],
seq_len(nrow(exprMatrNml)))
rownames(exprMatrNml) <- rownames(exprMatrTum) <- geneNames
nSdBelow <- 2
minPropPerGroup <- .2
rl <- receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup)
head(rl)

receptLoss documentation built on Nov. 8, 2020, 5:59 p.m.