Package 'DGEobj' reference manual

Title:	Differential Gene Expression (DGE) Analysis Results Data Object
Description:	Provides a flexible container to manage and annotate Differential Gene Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>). The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows by m-samples dimensions) and metadata (not keyed to row, col, or assays). A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified. Since the DGEobj is customizable and extensible it is not limited to RNA-seq analysis types of workflows -- it can accommodate nearly any data analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Authors:	John Thompson [aut], Connie Brett [aut, cre], Isaac Neuhaus [aut], Ryan Thompson [aut]
Maintainer:	Connie Brett <[email protected]>
License:	GPL-3
Version:	1.1.2
Built:	2024-11-04 04:04:23 UTC
Source:	https://github.com/cb4ds/dgeobj

DGEobj Package Overview

Description

DGEobj is an S3 data class that provides a flexible container for Differential Gene Expression (DGE) analysis results. The DGEobj class is designed to be extensible allowing definition of new data types as needed. A set of accessory functions to deposit, query and retrieve subsets of a data workflow has been provided. Attributes are used to capture metadata such as species and gene model, including reproducibility information such that a 3rd party can access a DGEobj history to see how each data object was created or modified.

Details

Operationally, the DGEobj is influenced by the RangedSummarizedExperiment (RSE). The DGEobj has data slots for row (gene), col (samples), assays (anything with n-rows by m-samples dimensions) and metadata (anything that can't be keyed to row, col or assay). The key motivation for creating the DGEobj data structure is that the RSE only allows one data item each in the row and col slots and thus is unsuitable for capturing the plethora of data objects created during a typical DGE workflow. The DGEobj data structure can hold any number of row and col data objects and thus is suitable for capturing the multiple steps of a downstream analysis.

Certain object types, primarily the count matrix and associated row and column info, are defined as unique which means only one instance of that type may be added to the DGEobj.

When multiple objects of one type are included in a DGEobj (e.g. two different fits), the concept of parent attributes is used to associate downstream data objects (e.g. contrasts) with the appropriate data object they are derived from.

More Information

browseVignettes(package = 'DGEobj')

Subset with square brackets

Description

Subset with square brackets

Usage

## S3 method for class 'DGEobj'
x[...]
## S3 method for class 'DGEobj'
x[...]

Arguments

`x`	A DGEobj
`...`	Additional parameters

Value

A DGEobj

Add a data item

Description

Add a data item

Usage

addItem(
  dgeObj,
  item,
  itemName,
  itemType,
  funArgs = match.call(),
  itemAttr,
  parent = "",
  overwrite = FALSE,
  init = FALSE
)
addItem(
  dgeObj,
  item,
  itemName,
  itemType,
  funArgs = match.call(),
  itemAttr,
  parent = "",
  overwrite = FALSE,
  init = FALSE
)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`item`	The data item to be deposited in the DGEobj
`itemName`	The user-assigned name for this data item
`itemType`	The type attribute. See showTypes() to see the predefined types – types are extensible with the newType() function.
`funArgs`	(optional) A text field to annotate how the data object was created. If the result of match.call() is passed as this argument, the name and arguments used in the current function are captured
`itemAttr`	(optional) A named list of attributes to add directly to the item
`parent`	(optional) itemName of the parent of this item
`overwrite`	Whether to overwrite a matching data object stored in the itemName slot (default = FALSE)
`init`	Internal Use (default = FALSE)

Value

A DGEobj

Examples

## Not run: 
   myFunArgs <- match.call()  #  Capture calling function and arguments

   myDGEobj <- addItem(myDGEobj, item     = MyCounts,
                                 itemName = "counts",
                                 itemType = "counts",
                                 funArgs  = myFunArgs)

## End(Not run)

## Not run: 
   myFunArgs <- match.call()  #  Capture calling function and arguments

   myDGEobj <- addItem(myDGEobj, item     = MyCounts,
                                 itemName = "counts",
                                 itemType = "counts",
                                 funArgs  = myFunArgs)

## End(Not run)

Add multiple data items

Description

Add multiple data items

Usage

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

## End(Not run)

## 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)

## End(Not run)

Add annotations

Description

Reads an annotation file containing key/value pairs or a named list and attaches them attributes to a DGEobj. If a file is used, it should be a text file containing key/value pairs separated by an equals sign. The keys argument specifies which keys we want to capture as attributes on the DGEobj.

Usage

annotateDGEobj(dgeObj, annotations, keys = NULL)
annotateDGEobj(dgeObj, annotations, keys = NULL)

Arguments

`dgeObj`	A object of class DGEobj created by function initDGEobj()
`annotations`	Either a character string path to a file with annotations given as key/value pairs separated by an equal sign, or a named list of key/value pairs
`keys`	By default (value = NULL), all keys are read in and applied as DGEobj attributes. Use the keys argument to specify a specific list of keys to read from the file.

Value

A DGEobj

Examples

   MyDgeObj <- system.file("exampleObj.RDS", package = "DGEobj")

## Not run: 
   #using a text file file of key=value pairs
   annotationFile <- "/location/to/myAnnotations.txt"
   MyDgeObj <- annotateDGEobj(MyDgeObj, annotationFile)

   #using a named list of key/values
   annotations <- list(Title     = "Rat Liver Slices from Bile Duct Ligation animals",
                       Organism  = "Rat",
                       GeneModel = "Ensembl.R89")
   MyDgeObj <- annotateDGEobj(MyDgeObj, annotations)

## End(Not run)

MyDgeObj <- system.file("exampleObj.RDS", package = "DGEobj")

## Not run: 
   #using a text file file of key=value pairs
   annotationFile <- "/location/to/myAnnotations.txt"
   MyDgeObj <- annotateDGEobj(MyDgeObj, annotationFile)

   #using a named list of key/values
   annotations <- list(Title     = "Rat Liver Slices from Bile Duct Ligation animals",
                       Organism  = "Rat",
                       GeneModel = "Ensembl.R89")
   MyDgeObj <- annotateDGEobj(MyDgeObj, annotations)

## End(Not run)

Cast as a simple list

Description

Cast as a simple list

Usage

## S3 method for class 'DGEobj'
as.list(x, ...)
## S3 method for class 'DGEobj'
as.list(x, ...)

Arguments

`x`	A DGEobj
`...`	Additional parameters

Value

A named list

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    mylist <- as.list(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    mylist <- as.list(exObj)

Get the baseType of an internal data item

Description

Get the baseType of an internal data item

Usage

baseType(dgeObj, type)
baseType(dgeObj, type)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`type`	An item type for which you want the baseType

Value

character string

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    baseType(exObj, type = "DGEList")

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    baseType(exObj, type = "DGEList")

Get a list of the available baseTypes

Description

Get a list of the available baseTypes

Usage

baseTypes(dgeObj)
baseTypes(dgeObj)

Arguments

dgeObj

(optional) A class DGEobj created by function initDGEobj()

Value

A character vector of baseTypes

Examples

    # Global definition of baseTypes
    baseTypes()

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # Basetypes from a specific DGEobj
    baseTypes(exObj)

# Global definition of baseTypes
    baseTypes()

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # Basetypes from a specific DGEobj
    baseTypes(exObj)

Get the "assay" dimensions (row/genes by col/samples)

Description

Returns the dimensions of the assay data (baseType)

Usage

## S3 method for class 'DGEobj'
dim(x)
## S3 method for class 'DGEobj'
dim(x)

Arguments

`x`	A class DGEobj created by function initDGEobj()

Value

An integer vector [r,c] with a length of 2.

Get the "assay" names (row/genes by col/samples)

Description

Returns a list of length 2 containing the the assay data names (baseType)

Usage

## S3 method for class 'DGEobj'
dimnames(x)
## S3 method for class 'DGEobj'
dimnames(x)

Arguments

`x`	A class DGEobj created by function initDGEobj()

Value

A list of length 2 containing rownames and colnames of the DGEobj

Get all attributes

Description

Get all user-defined attributes from a DGEobj except for any listed in the excludeList argument.

Usage

getAttributes(
  dgeObj,
  excludeList = list("dim", "dimnames", "names", "row.names", "class")
)
getAttributes(
  dgeObj,
  excludeList = list("dim", "dimnames", "names", "row.names", "class")
)

Arguments

`dgeObj`	A DGEobj
`excludeList`	A list of attribute names to exclude from the output (default = list("dim", "dimnames", "names", "row.names"))

Value

A named list

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    getAttributes(exObj)

    # Get the formula attribute from the design (if set)
    attr(exObj$design, "formula")

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    getAttributes(exObj)

    # Get the formula attribute from the design (if set)
    attr(exObj$design, "formula")

Retrieve data items by baseType

Description

Retrieve data items by baseType

Usage

getBaseType(dgeObj, baseType)
getBaseType(dgeObj, baseType)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`baseType`	One or more of: ["row", "col", "assay", "meta"]

Value

A list of data items

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    Assays <- getBaseType(exObj, baseType = "assay")
    AssaysAndMeta <- getBaseType(exObj, c("assay", "meta"))

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    Assays <- getBaseType(exObj, baseType = "assay")
    AssaysAndMeta <- getBaseType(exObj, c("assay", "meta"))

Retrieve a data item by name

Description

Retrieve a data item by name

Usage

getItem(dgeObj, itemName)
getItem(dgeObj, itemName)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`itemName`	Name of item to retrieve

Value

The requested data item

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    MyCounts <- getItem(exObj, "counts")

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    MyCounts <- getItem(exObj, "counts")

Retrieve multiple data items by name

Description

Retrieve multiple data items by name

Usage

getItems(dgeObj, itemNames)
getItems(dgeObj, itemNames)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`itemNames`	A character string, character vector, or list names to retrieve

Value

A list

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    myList <- getItems(exObj, list("counts", "geneData"))
    names(myList)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    myList <- getItems(exObj, list("counts", "geneData"))
    names(myList)

Retrieve data items by type

Description

Retrieve data items by type

Usage

getType(dgeObj, type, parent)
getType(dgeObj, type, parent)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`type`	A type or list of types to retrieve
`parent`	(optional) Filter return list for common parent (e.g. useful to select one set of contrast results when multiple fits have been performed)

Value

A list of data items

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    MyRawData      <- getType(exObj, type = list("counts", "design", "geneData"))

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    MyRawData      <- getType(exObj, type = list("counts", "design", "geneData"))

Initialize with base data (primaryAssayData, row annotations, col annotations)

Description

Initialize with base data (primaryAssayData, row annotations, col annotations)

Usage

initDGEobj(
  primaryAssayData,
  rowData,
  colData,
  level,
  customAttr,
  allowShortSampleIDs = FALSE,
  DGEobjDef = initDGEobjDef()
)
initDGEobj(
  primaryAssayData,
  rowData,
  colData,
  level,
  customAttr,
  allowShortSampleIDs = FALSE,
  DGEobjDef = initDGEobjDef()
)

Arguments

`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.

Value

A DGEobj

Examples

   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"))

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"))

Instantiate a class DGEobjDef object.

Description

Instantiate a class DGEobjDef object.

Usage

initDGEobjDef(levels, primaryAssayNames, types, uniqueTypes)
initDGEobjDef(levels, primaryAssayNames, types, uniqueTypes)

Arguments

`levels`	A character string or vector providing names for new levels
`primaryAssayNames`	A character string or vector, must be the same length as levels This argument supplies the primaryAssayNames for the corresponding levels.
`types`	A named character vector of new types where the values indicate the basetype for each named type (optional)
`uniqueTypes`	A name or vector of names to add to the uniqueType list (optional)

Value

A class DGEobjDef object suitable for use with initDGEobj

Examples

    # return the default DGEobj definition
    myDGEobjDef <- initDGEobjDef()

    # Optionally add some new types and levels for metabolomics data
     myDGEobjDef <- initDGEobjDef(levels = "metabolomics",
                                  primaryAssayNames = "intensity",
                                  types <- c(normalizedIntensity = "assay"))

    # When a new level is defined, the itemNames and types for the
    # rowData and colData are automatically established.  The
    # types argument is only needed to define downstream workflow objects.

# return the default DGEobj definition
    myDGEobjDef <- initDGEobjDef()

    # Optionally add some new types and levels for metabolomics data
     myDGEobjDef <- initDGEobjDef(levels = "metabolomics",
                                  primaryAssayNames = "intensity",
                                  types <- c(normalizedIntensity = "assay"))

    # When a new level is defined, the itemNames and types for the
    # rowData and colData are automatically established.  The
    # types argument is only needed to define downstream workflow objects.

Retrieve the object inventory

Description

Retrieve the object inventory

Usage

inventory(dgeObj, verbose = FALSE)
inventory(dgeObj, verbose = FALSE)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`verbose`	Include funArgs column in the output (default = FALSE)

Value

A data.frame summarizing the data contained in the DGEobj

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    inventory(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    inventory(exObj)

Add a new type definition to a DGEobj

Description

Add a new type definition to a DGEobj

Usage

newType(dgeObj, itemType, baseType, uniqueItem = FALSE)
newType(dgeObj, itemType, baseType, uniqueItem = FALSE)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`itemType`	The name of the new type to create
`baseType`	The baseType of the new item. One of [row, col, assay, meta]
`uniqueItem`	If set to TRUE, only one instance of the new type is allowed in a DGEobj

Value

A DGEobj

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- newType(exObj,
                     itemType   = "AffyRMA",
                     baseType   = "assay",
                     uniqueItem = TRUE)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- newType(exObj,
                     itemType   = "AffyRMA",
                     baseType   = "assay",
                     uniqueItem = TRUE)

Print the Inventory

Description

Print the Inventory

Usage

## S3 method for class 'DGEobj'
print(x, ..., verbose = FALSE)
## S3 method for class 'DGEobj'
print(x, ..., verbose = FALSE)

Arguments

`x`	A class DGEobj created by function initDGEobj()
`...`	Additional parameters
`verbose`	Include funArgs column in the output (default = FALSE)

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    print(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    print(exObj)

Reset to original data

Description

During a workflow, a DGEobj typically gets filtered down to remove samples that fail QC or non-expressed genes. The resetDGEobj() function produces a new DGEobj with the original unfiltered data. Resetting an object does not restore changes to attributes or class, but does revert changes made with addItem() and rmItem(). Reset requires that *_orig data is still in the DGEobj.

Usage

resetDGEobj(dgeObj)
resetDGEobj(dgeObj)

Arguments

dgeObj

A class DGEobj created by function initDGEobj()

Value

A DGEobj

Examples

    #example object
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # subset to first 10 rows to show reset functionality
    exObj <- exObj[c(1:10), ]

    exObj <- resetDGEobj(exObj)
    dim(exObj)

#example object
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # subset to first 10 rows to show reset functionality
    exObj <- exObj[c(1:10), ]

    exObj <- resetDGEobj(exObj)
    dim(exObj)

Removes a named data item

Description

Removes a named data item

Usage

rmItem(dgeObj, itemName)
rmItem(dgeObj, itemName)

Arguments

`dgeObj`	A class DGEobj created by function initDGEobj()
`itemName`	Name of the item to remove

Value

A DGEobj

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- rmItem(exObj, "design")

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- rmItem(exObj, "design")

Set attributes

Description

Set one or more attributes on a DGEobj or on a specific item within a DGEobj.

Usage

setAttributes(dgeObj, attribs)
setAttributes(dgeObj, attribs)

Arguments

`dgeObj`	A DGEobj
`attribs`	A named list of attribute/value pairs

Details

This function adds attributes without deleting the attributes that are already present. Any named attribute that already exists in the object will be updated. To remove an attribute from an object pass NULL as the attribute value.

Value

A DGEobj

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # Assign attributes to a DGEobj
    MyAttributes <- list(Platform       = "RNA-Seq",
                         Instrument     = "HiSeq",
                         Vendor         = "Unknown",
                         readType       = "PE",
                         readLength     = 75,
                         strandSpecific = TRUE)
    exObj <- setAttributes(exObj, MyAttributes)

    # Set attributes on an item inside a DGEobj
    MyAttributes <- list(normalized   = FALSE,
                         LowIntFilter = "FPK >5 in >= 1 group")
    exObj[["counts"]] <- setAttributes(exObj[["counts"]], MyAttributes)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    # Assign attributes to a DGEobj
    MyAttributes <- list(Platform       = "RNA-Seq",
                         Instrument     = "HiSeq",
                         Vendor         = "Unknown",
                         readType       = "PE",
                         readLength     = 75,
                         strandSpecific = TRUE)
    exObj <- setAttributes(exObj, MyAttributes)

    # Set attributes on an item inside a DGEobj
    MyAttributes <- list(normalized   = FALSE,
                         LowIntFilter = "FPK >5 in >= 1 group")
    exObj[["counts"]] <- setAttributes(exObj[["counts"]], MyAttributes)

Print attributes

Description

This function prints all attributes regardless of the class of the attribute value.

Usage

showAttributes(
  dgeObj,
  skipList = c("dim", "dimnames", "rownames", "colnames", "listData", "objDef")
)
showAttributes(
  dgeObj,
  skipList = c("dim", "dimnames", "rownames", "colnames", "listData", "objDef")
)

Arguments

`dgeObj`	A DGEobj
`skipList`	A character vector of attributes to skip. Use this to avoid printing certain lengthy attributes like rownames. Defaults to c("dim", "dimnames", "rownames", "colnames", "listData", "objDef")

Details

*Note* Use showMeta() to only retrieve attributes that are key/value pairs.

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

   showAttributes(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

   showAttributes(exObj)

Retrieve the Key/Value metadata attributes that have a character value and length of 1

Description

Retrieve the Key/Value metadata attributes that have a character value and length of 1

Usage

showMeta(dgeObj)
showMeta(dgeObj)

Arguments

dgeObj

A DGEobj with attributes

Value

A data.frame with "Attribute" and "Value" columns

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    showMeta(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    showMeta(exObj)

Returns and prints the list of all defined types

Description

Returns and prints the list of all defined types

Usage

showTypes(dgeObj)
showTypes(dgeObj)

Arguments

dgeObj

A class DGEobj created by function initDGEobj()

Value

data.frame

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    showTypes(exObj)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    showTypes(exObj)

Subset internal row or column data

Description

Subset internal row or column data

Usage

## S3 method for class 'DGEobj'
subset(x, ..., row, col, drop = FALSE, debug = FALSE)
## S3 method for class 'DGEobj'
subset(x, ..., row, col, drop = FALSE, debug = FALSE)

Arguments

`x`	A class DGEobj created by function initDGEobj()
`...`	Additional parameters
`row`	Row index for the subset
`col`	Col index for the subset
`drop`	Included for compatibility only
`debug`	(default = FALSE) Set to TRUE to get additional information on the console if subsetting a DGEobj fails with a dimension error.

Value

A DGEobj

Examples

    # example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- subset(exObj, 1:10, 5:50)

# example DGEobj
    exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))

    exObj <- subset(exObj, 1:10, 5:50)

Package 'DGEobj'

Help Index

DGEobj Package Overview

Description

Details

More Information

Subset with square brackets

Description

Usage

Arguments

Value

Add a data item

Description

Usage

Arguments

Value

Examples

Add multiple data items

Description

Usage

Arguments

Value

Examples

Add annotations

Description

Usage

Arguments

Value

Examples

Cast as a simple list

Description

Usage

Arguments

Value

Examples

Get the baseType of an internal data item

Description

Usage

Arguments

Value

Examples

Get a list of the available baseTypes

Description

Usage

Arguments

Value

Examples

Get the "assay" dimensions (row/genes by col/samples)

Description

Usage

Arguments

Value

Get the "assay" names (row/genes by col/samples)

Description

Usage

Arguments

Value

Get all attributes

Description

Usage

Arguments

Value

Examples

Retrieve data items by baseType

Description

Usage

Arguments

Value

Examples

Retrieve a data item by name

Description

Usage

Arguments

Value

Examples

Retrieve multiple data items by name

Description

Usage

Arguments

Value