runDESeq2: runDESeq2

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Wrapper for DESeq2.

Usage

runDESeq2(object, group = NULL, condition.a = NULL,
  condition.b = NULL, fitType = c("parametric", "local", "mean"),
  ngenes = NULL)

Arguments

object	An EMSet
group	Column in colInfo that contains a set of conditions you want to test
condition.a	Condition(s) in the group column that you want to test for.
condition.b	Condition(s) in the group column that you want to test against.
fitType	Type of fit to use with DESeq2 - parametric, local (Default) and mean.
ngenes	Number of genes you want to test (Default: all genes)

Details

This is a wrapper for DESeq2. The function handles the conversion of the EMSet to a DESeqDataset object for use with the DESeq2 functions.

Value

Results from DESeq2

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.