Wrapper for limma-voom workflow — voom

For generating statistics for 'seqData' objects

voom_wrapper(
  omicsData,
  p_adjust = "BH",
  comparisons = NULL,
  p_cutoff = 0.05,
  ...
)

Arguments

omicsData: an object of type 'seqData', created by as.seqData
p_adjust: Character string for p-value correction method, refer to ?p.adjust() for valid options
comparisons: `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.
p_cutoff: 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.

Value

statRes object

Details

Runs default limma-voom workflow using empirical Bayes moderated t-statistics. Additional arguments can be passed for use in the function, refer to calcNormFactors() in edgeR package.

References

Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47.