runTests: Runs a differential expression analysis.

Description Usage Arguments Value

View source: R/function.diff.R

Description

Runs a differential expression analysis using the selected method. This is used by the differentialExpression function. This is simply a wrapper to make sure that the different analysis methods use the same normalization method and return results in the same format.

Usage

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runTests(data, groups, norm = "TMM", de = "edgeR",
  homogenize.mixes = TRUE)

Arguments

data

The expression matrix or data.frame, with gene symbols or transcript Refseq IDs as row.names.

groups

A logical vector (or coercible to logical) of length ncol(data), indicating to which group each sample (i.e. column in 'data') belongs. There can be only two groups.

norm

The normalization method to use (either "linear", or any of the methods supported by edgeR's calcNormFactors. Defaults to 'TMM'.

de

The differential expression method to use. Either 'edgeR', 'DESeq', 'DESeq2', 'EBSeq', 'voom', 't' (t-test), or 'logt' (t-test on log-transformed values). A string indicating the unit of the expression matrix (either "FPKM", "TPM" or "COUNTS").

homogenize.mixes

logical, whether the two spike-in mixes should be homogenized for the purpose of calculating normalization factors.

Value

A data.frame with the results of the differential expression analysis.


plger/RNAontheBENCH documentation built on May 25, 2019, 8:22 a.m.