ds.DESeq2: Server-side Differential Gene Expression analysis using...

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Server-side Differential Gene Expression analysis using DESeq2

Description

This function performs a non-disclosive Differential Gene Expression Analysis using DESeq2 package from Bioconductor.

Usage

ds.DESeq2(
  model,
  set,
  test = "Wald",
  fitType = "parametric",
  sfType = "ratio",
  reduced = NULL,
  contrast = NULL,
  datasources = NULL
)

Arguments

model	formula indicating the condition and other covariates to be ajusted
set	a RangedSummarizedExperiment object.
test	"Wald" or "LRT".
fitType	"parametric", "local", or "mean".
sfType	"ratio", "poscounts", or "iterate".
reduced	a reduced formula for test="LRT"
contrast	the comparison to extract from the object to build the results table
datasources	a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Details

Implementation of Bioconductor's DESeq2 in DataSHIELD infraestructure.

This function is similar to Bioconductor's DESeq2 package DESeq function.

Value

Data frame containing the results of the Differential Gene Expression analysis

Author(s)

L. Abarrategui, for DataSHIELD development team

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.