limmaDS: Differential expression analysis using limma on the...

View source: R/limmaDS.R

limmaDSR Documentation

Differential expression analysis using limma on the server-side

Description

Performs differential expression analysis using LIMMA

Usage

limmaDS(
  Set,
  variable_names,
  covariable_names,
  type,
  contrasts,
  levels,
  coef,
  sva,
  annotCols,
  method,
  robust,
  normalization,
  voomQualityWeights,
  big,
  sort.by
)

Arguments

Set

either a ExpressionSet or a RangedSummarizedExperiment

variable_names

grouping variable used to perform differential expression analysis

covariable_names

name of variables used in the adjusted models

type

...

contrasts

...

levels

...

coef

...

sva

should differential expression analysis be adjusted by SVA?

annotCols

variables from the annotation data used in the output

method

String indicating the method used in the regression (e.g. lmFit function of limma: "ls" or "robust". (Default: "ls")

robust

Logical value indicating whether robust method is applied in the eBayes function of limma. Default is FALSE.

normalization

String indicating the normalize method used when using voom for RNAseq data (see normalized.method argument in limma::vomm)

voomQualityWeights

Logical value indicating whether limma::voomWithQualityWeights should be used instead of limma::voom.

big

Logical value indicating whether SmartSVA should be used instead of SVA (TRUE recommended for methylation or when having large number of samples).

Value

a matrix with genes ordered by p-value

Author(s)

Gonzalez, JR.


isglobal-brge/dsOmics documentation built on Nov. 11, 2024, 4:18 a.m.