Execute edgeR expression Analisys

Usage

runLimma(
  countMatrix,
  numberReplics,
  designExperiment,
  methodNorm = "TMM",
  methodAdjPvalue = "BH",
  numberTopTable = 1e+06
)

Arguments

countMatrix: either a matrix of raw (read) counts.
numberReplics: number of replicate (technical or biologcal) integer
designExperiment: replicate and treatment by samples
methodNorm: normalization method to be used
methodAdjPvalue: correction method, a character string. Can be abbreviated.
numberTopTable: maximum number of genes to list

Value

limma report in data Frame fromat

Examples

set.seed(42)
counts <- matrix(
  as.integer(c(
    rnbinom(200, mu = 10, size = 1),
    rnbinom(200, mu = 100, size = 1)
  )),
  nrow = 100,
  dimnames = list(
    paste0("gene", seq_len(100)),
    paste0("sample", seq_len(4))
  )
)
groups_info <- c("control", "control", "treated", "treated")
treats <- c("control", "treated")
toolResult <- NULL
toolResult$limma <- runLimma(counts, 2, rep(treats, each = 2))
#> calcNormFactors has been renamed to normLibSizes
#> Removing intercept from test coefficients