Wrapper of edgeR procedure

Usage

edgeRDE(
  counts,
  group,
  norm.factors = NULL,
  adjust.factors = NULL,
  design.formula = NULL,
  contrast.df = NULL,
  coef = NULL,
  logfc.cutoff = 1,
  p.cutoff = 0.05,
  prior.count = 0.125,
  only.pos = TRUE
)

Arguments

counts: A un-normalized counts data matrix.
group: Vector of length p mapping the columns of counts to corresponding samples group.
norm.factors: Vector of normalization factors with p length.
adjust.factors: Matrix with each column indicates the adjusting factors that estimated from RUV.
design.formula: Formula
contrast.df: Data frame of contrast, where extracting results as first column vs. second column.
coef: Integer or character vector indicating which coefficients of the linear model are to be tested equal to zero. Values must be columns or column names of design.
logfc.cutoff: Filter genes by at least X-fold difference (log2-scale) between the two groups of samples, default: 1.
p.cutoff: Filter genes by no more than Y adjusted p-value, default: 0.05.
prior.count: Average prior count to be added to observation to shrink the estimated log-fold-changes towards zero, default: 0.125.
only.pos: Only return positive genes in filtered results res.sig.ls, default: TRUE.

Value

List containing differential analysis object, result table and filtered result table.