DGEobj (version 1.1.2)

addItems: Add multiple data items

Description

Add multiple data items

Usage

addItems(dgeObj, itemList, itemTypes, parents, itemAttr, overwrite = FALSE)

Arguments

dgeObj

A class DGEobj created by function initDGEobj()

itemList

A named list of data items to add to DGEobj

itemTypes

A list of type values for each item on itemList

parents

(optional) A list of parent values for each item on itemList (optional, but highly recommended)

itemAttr

(optional) An named list of attributes to add to each item. These attributes will be attached to all items in the call.

overwrite

Whether to overwrite a matching data object stored in the itemName slot (default = FALSE)

Value

A DGEobj

Examples

# NOT RUN {
   # NOTE: Requires the edgeR package

   # Add normalized counts and log2CPM as additional "assay" items in the DGEobj
   dgeObj  <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   dgeList <- edgeR::calcNormFactors(edgeR::DGEList(dgeObj$counts), method="TMM")
   log2cpm <- edgeR::cpm(dgeList, log = TRUE)

   dgeObj <- addItems(dgeObj,
                      itemList = list(newDgelist = dgeList, Log2CPM = log2cpm),
                      itemTypes = list("assay", "assay"),
                      parents = list("counts", "newDgelist")
   )
   inventory(dgeObj)
# }
# NOT RUN {
# }