dataInfo: Class 'dataInfo'

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Class dataInfo

Description

This was the class for storing input data for workflow. We now generally recommend using the Create_DEGContainer to create it in DEGContainer obj.

contains configurations info of RNAseqStat2

Usage

species(obj)

dataType(obj)

idType(obj)

expMatrix(obj)

groupInfo(obj)

caseGroup(obj)

filterMethod(obj)

matrixFiltered(obj)

geneNames(obj, filtered)

sampleNames(obj, filtered)

species(obj) <- value

dataType(obj) <- value

idType(obj) <- value

expMatrix(obj) <- value

groupInfo(obj) <- value

caseGroup(obj) <- value

filterMethod(obj) <- value

matrixFiltered(obj) <- value

geneNames(obj, filtered) <- value

sampleNames(obj, filtered) <- value

Value

The accessor functions species, dataType,
idType, expMatrix, groupInfo,
caseGroup, filterMethod, matrixFiltered
return the corresponding elements of a
DEGContainer or dataInfo.

Slots

species

species for your data. 'Human' or 'Mouse'.

dataType

kind of expresses value matrix. 'Counts' (Integer) or 'Array' (Decimal).

idType

kind of gene id. 'ENSEMBL' or 'SYMBOL', If 'ENSEMBL', 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'.

matrixFiltered

expresses value matrix after apply filterMethod. Should be a data.frame row named by gene ID and column named by Sample

See Also

Other DEGContainer: MSigDB, degResults-class

Other DEGContainer: MSigDB, degResults-class

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