Description Usage Arguments Value
View source: R/function.diff.R
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.
1 2 |
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 |
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. |
A data.frame with the results of the differential expression analysis.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.