runDESeq: runDESeq

Description Usage Arguments Value Examples

View source: R/deseq2.R

Description

Run DESeq2 algorithm on the selected conditions. Output is to be used for the interactive display.

Usage

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runDESeq(data, columns, conds, fitType = c("parametric", "local", "mean"),
  non_expressed_cutoff = 10)

Arguments

data,

A matrix that includes all the expression raw counts, rownames has to be the gene, isoform or region names/IDs

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

fitType,

DESeq2 fitType, it can be 'parametric', 'local', 'mean'.

non_expressed_cutoff,

to remove unexpressed regions/genes/isoforms this cutoff is used

Value

deseq2 results

Examples

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    x <- runDESeq(data<-NULL, columns<-c())

debrowser documentation built on May 2, 2018, 3:36 a.m.