DGEobj (version 1.0.1)

initDGEobj: Initialize with base data (counts, gene annotations, sample annotations)

Description

Initialize with base data (counts, gene annotations, sample annotations)

Usage

initDGEobj(
  counts,
  rowData,
  colData,
  level,
  customAttr,
  allowShortSampleIDs = FALSE,
  DGEobjDef = .DGEobjDef
)

Arguments

counts

A count matrix or dataframe with row and colnames

rowData

Gene, isoform or exon level annotation. Rownames must match the rownames in count matrix

colData

A dataframe describing the experiment design. Rownames much match the colnames(counts)

level

One of "gene", "isoform", or "exon"

customAttr

(optional) Named list of attributes

allowShortSampleIDs

Using sequential integer rownames (even if typed as character) is discouraged and by default will abort the DGEobj creation. If you have a legitimate need to have short sample names composed of numeric characters, you can set this argument to TRUE (default = FALSE)

DGEobjDef

An object definition. Defaults to the global DGEobj definition (.DGEobjDef) and you usually shouldn't change this unless you're customizing the object for new data types.

Value

A DGEobj

Examples

# NOT RUN {
   # Initialize a DGEobj
   myDgeObj <- initDGEobj(counts = MyCounts,
                          rowData = MyGeneAnnotation,
                          colData = MyDesign,
                          level = "gene",
                          customAttr = list (Genome = "Mouse.B38",
                                             GeneModel = "Ensembl.R84"))
# }
# NOT RUN {
# }