nbinomTest {DESeq} | R Documentation |
This function tests for differences between the base means of two conditions (i.e., for differential expression in the case of RNA-Seq).
nbinomTest(cds, condA, condB, pvals_only = FALSE, eps=NULL )
cds |
a CountDataSet with size factors and raw variance functions |
condA |
one of the conditions in 'cds' |
condB |
another one of the conditions in 'cds' |
pvals_only |
return only a vector of (unadjusted) p values instead of the data frame described below. |
eps |
This argument is no longer used. Do not use it. |
See nbinomTestForMatrices
for more technical informations
A data frame with the following columns:
id |
The ID of the observable, taken from the row names of the counts slots. |
baseMean |
The base mean (i.e., mean of the counts divided by the size factors) for the counts for both conditions |
baseMeanA |
The base mean (i.e., mean of the counts divided by the size factors) for the counts for condition A |
baseMeanB |
The base mean for condition B |
foldChange |
The ratio meanB/meanA |
log2FoldChange |
The log2 of the fold change |
pval |
The p value for rejecting the null hypothesis 'meanA==meanB' |
padj |
The adjusted p values (adjusted with 'p.adjust( pval, method="BH")') |
Simon Anders, sanders@fs.tum.de
cds <- makeExampleCountDataSet() cds <- estimateSizeFactors( cds ) cds <- estimateDispersions( cds ) head( nbinomTest( cds, "A", "B" ) )