edgeR_wrapper {pmartR}

Wrapper for edgeR workflow

Description

For generating statistics for 'seqData' objects.

Usage

edgeR_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. Defaults to "BH" (Benjamini & Hochberg).

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

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.

Value

statRes object

References

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.