loadData: loadData

In askomics/askoR: askoR - Differential Expresion Analysis using edgeR

loadData

Description

Function to load :

• Count data (one of this below):

  • count matrix : 1 file with all counts for each samples/conditions or multiple

  • list of files : 1 file of count per conditions, files names contained in sample file

• Metatdata :

  • sample file : file describing the samples and the experimental design

  • contrast file : matrix which specifies which comparisons you would like to make between the samples

  • (optional) annotation file : functional/genomic annotation for each genes

  • (optional) GO terms annotations files : GO annotations for each genes

Three output directory will be create :

• images : contains all the images created when running this pipeline with the exception of the upsetR and Venn graphs.

• vennDiagram : contain all venn diagrams created by VD function

• UpSetR_graphs : contain all upset graphs created by UpSetGraph function

• Askomics : files compatible with Askomics Software

Usage

loadData(parameters)

Arguments

parameters

list that contains all arguments charged in Asko_start

Value

data, list contain all data and metadata (DGEList, samples descriptions, contrast, design and annotations)

Examples

## Not run: 
    parameters<-Asko_start()
    data<-loadData(parameters)

## End(Not run)

askomics/askoR documentation built on Aug. 11, 2024, 11:05 p.m.