For generating statistics for 'seqData' objects.
edgeR_wrapper(
omicsData,
p_adjust = "BH",
comparisons = NULL,
p_cutoff = 0.05,
...
)an object of type 'seqData', created by
as.seqData
Character string for p-value correction method, refer to ?p.adjust() for valid options. Defaults to "BH" (Benjamini & Hochberg).
`data.frame` with columns for "Control" and "Test" containing the different comparisons of interest. Comparisons will be made between the Test and the corresponding Control If left NULL, then all pairwise comparisons are executed.
Numeric value between 0 and 1 for setting p-value significance threshold
additional arguments passed to methods functions. Note, formatting option changes will interfere with wrapping functionality.
statRes object
Requires the 'edgeR' and 'limma' packages. Runs default edgeR workflow with empirical Bayes quasi-likelihood F-tests. Additional arguments can be passed for use in the function, refer to calcNormFactors() and glmQLFit() in edgeR package.
Flags (signatures) - Indicator of statistical significance for computed test. Zeroes indicate no significance, while +/- 1 indicates direction of significance.
Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.