runLimma: runLimma

In UMMS-Biocore/debrowser: Interactive Differential Expresion Analysis Browser

runLimma

Description

Run Limma algorithm on the selected conditions. Output is to be used for the interactive display.

Usage

runLimma(
  data = NULL,
  metadata = NULL,
  columns = NULL,
  conds = NULL,
  params = NULL
)

Arguments

data,	A matrix that includes all the expression raw counts, rownames has to be the gene, isoform or region names/IDs
metadata,	metadata of the matrix of expression raw counts
columns,	is a vector that includes the columns that are going to be analyzed. These columns has to match with the given data.
conds,	experimental conditions. The order has to match with the column order
params,	normfact: Calculate normalization factors to scale the raw library sizes. Values can be "TMM","RLE","upperquartile","none". fitType, fitting method; "ls" for least squares or "robust" for robust regression normBet: Normalizes expression intensities so that the intensities or log-ratios have similar distributions across a set of arrays.

Value

Limma results

Examples

    x <- runLimma()

UMMS-Biocore/debrowser documentation built on Feb. 9, 2024, 6:15 p.m.