Create_DEGContainer: Create 'DEGContainer'

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Create DEGContainer

Description

Begin in DEGContainer.

Usage

Create_DEGContainer(
  species = "Human",
  dataType = "Counts",
  idType = "SYMBOL",
  expMatrix,
  groupInfo,
  caseGroup,
  filterMethod = "rowSums(expMatrix > 0) >= ncol(expMatrix)/2",
  msi_species = NULL,
  msi_category = "H",
  OrgDb = NULL,
  organism = NULL,
  GOTERM2GENE = NULL,
  GOTERM2NAME = NA,
  KEGGTERM2GENE = NULL,
  KEGGTERM2NAME = NA
)

Arguments

species	species for your data.
dataType	kind of expresses value matrix. 'Counts' (Integer) or 'Array' (Decimal).
idType	kind of gene id. 'ENSEMBL' or 'SYMBOL', If 'ENSEMBL',species supposed be one of ('Human', 'Mouse' and 'Rat'), it will be automatically converted to 'SYMBOL'.
expMatrix	expresses value matrix. Should be a data.frame row named by gene ID and column named by Sample
groupInfo	a Character Vectors ordered by samples in matrix.
caseGroup	a Character names of case group.
filterMethod	a function used to filter expresses value matrix. Or disable filter by set as 'NULL'.
msi_species	one of msigdbr_species
msi_category	MSigDB collection abbreviation, such as H or C1.
OrgDb	Select an OrgDb.
organism	Select an organism.
GOTERM2GENE	custom enrich data of GO.
GOTERM2NAME	custom enrich data of GO.
KEGGTERM2GENE	custom enrich data of GSE.
KEGGTERM2NAME	custom enrich data of GSE.

Details

'Human', 'Mouse' and 'Rat' is full supported. For other species, more setting is needed.
If data can't provided, related steps in workflow will ignore.
OrgDb can be find from here https://bioconductor.org/packages/release/BiocViews.html#___OrgDb
organism can be find from here https://www.genome.jp/kegg/catalog/org_list.html
msi_species can be get from msigdbr_species

Value

a DEGContainer object

Examples

Create_DEGContainer(expMatrix = counts_input,groupInfo = c("C","C","C","T","T","T"),caseGroup = "T")

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.