voom_wrapper {pmartR}

Wrapper for limma-voom workflow

Description

For generating statistics for 'seqData' objects

Usage

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.

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.

Value

statRes object

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.