initDGEobj | R Documentation |
Initialize with base data (primaryAssayData, row annotations, col annotations)
initDGEobj( primaryAssayData, rowData, colData, level, customAttr, allowShortSampleIDs = FALSE, DGEobjDef = initDGEobjDef() )
primaryAssayData |
A numeric matrix or dataframe with row and colnames. Each column represents a sample. Each row represents and assay. This is typically the counts matrix in a DGE RNA-Seq experiment. |
rowData |
Gene, exon, isoform or protein level annotation. Rownames must match the rownames in primaryAssayData |
colData |
A dataframe describing the experiment design. Rownames much match the colnames(primaryAssayData) |
level |
One of "gene", "exon", "isoform" or "protein" |
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 (initDGEobjDef()) and you usually shouldn't change this unless you're customizing the object for new data types. |
A DGEobj
dgeObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj")) MyCounts <- dgeObj$counts geneinfo <- dgeObj$geneData sampinfo <- dgeObj$design myDgeObj <- initDGEobj(primaryAssayData = MyCounts, rowData = geneinfo, colData = sampinfo, level = "gene", customAttr = list (Genome = "Rat.B6.0", GeneModel = "Ensembl.R89"))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.