Calculate P-values of Differential Expression

Description

A function called within SimData. Calculates the P-value of differential expression for each gene under either Wilcoxin signed rank test (paired data) or rank sum test (unpaired data). The vector of differences used in the test is based off of the log of the counts for each gene plus 1 divided by their respective multiplicative normalization factors provided by the user.

Usage

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CalcPvalWilcox(counts, treatment, replic = NULL, sort.method, 
               sorted = FALSE, norm.factors, exact = FALSE)

Arguments

counts

A matrix of counts where each row specifies a gene and each column specifies a replicate.

treatment

A vector specifying the treatment group for each column of the counts matrix. Only two treatment groups of either paired or unpaired data are allowed.

replic

A vector specifying the replicate for each column of the counts matrix when there is paired data; optional if data is unpaired.

sort.method

Character vector specifying one of "unpaired" or "paired", depending on the structure of the data.

sorted

logical vector specifying whether data has already gone through SortData function. Defaults to FALSE.

norm.factors

A positive numeric vector of multiplicative normalization factors for each column of the counts matrix.

exact

Specifies whether an exact signed rank test (paired) or exact ranksum test (unpaired) should be used.

Value

probs: a vector of p-values of differential expression for each gene.

Author(s)

Samuel Benidt <sgbenidt@gmail.com>