deNanostring: deNanostring

In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Description

Runs a differential expression analysis and compares it to a log-t-test performed on the nanostring data.

Usage

deNanostring(rnaseq = NULL, method = "edgeR", norm = "TMM",
  quantification = "", threshold = 0.01)

Arguments

rnaseq	Either the (gene-level) count matrix, or a character indicating the location of the file.
method	The differential expression method to use. Either 'edgeR', 'DESeq', 'DESeq2', 'EBSeq', 'voom', 't' (t-test), or 'logt' (t-test on log-transformed values).
norm	The normalization method to use (either "linear", or any of the methods supported by edgeR's calcNormFactors. Defaults to 'TMM'.
quantification	A string indicating the quantification that was used to produce the expression matrix (use for labeling)
threshold	The p-value threshold applied on the Nanostring data to identify whether a gene is differentially-expressed or not.

Value

A deNanostring.compare plot

Examples

data(exampledata)
deNanostring(exampleGeneLevel, method="edgeR", norm="TMM", 
  quantification="Tophat-featureCounts")

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