HandleMetaData: Handling _meta-data_ in 'COTAN' objects

In seriph78/COTAN: COexpression Tables ANalysis

Handling meta-data in COTAN objects

Description

Much of the information stored in the COTAN object is compacted into three data.frames:

• "metaDataset" - contains all general information about the data-set

• "metaGenes" - contains genes' related information along the lambda and dispersion vectors and the fully-expressed flag

• "metaCells" - contains cells' related information along the nu vector, the fully-expressing flag, the clusterizations and the conditions

Usage

## S4 method for signature 'COTAN'
getMetadataDataset(objCOTAN)

## S4 method for signature 'COTAN'
getMetadataElement(objCOTAN, tag)

## S4 method for signature 'COTAN'
getMetadataGenes(objCOTAN)

## S4 method for signature 'COTAN'
getMetadataCells(objCOTAN)

## S4 method for signature 'COTAN'
getDims(objCOTAN)

datasetTags()

## S4 method for signature 'COTAN'
initializeMetaDataset(objCOTAN, GEO, sequencingMethod, sampleCondition)

## S4 method for signature 'COTAN'
addElementToMetaDataset(objCOTAN, tag, value)

getColumnFromDF(df, colName)

setColumnInDF(df, colToSet, colName, rowNames = vector(mode = "character"))

Arguments

objCOTAN	a COTAN object
tag	the new information tag
GEO	a code reporting the GEO identification or other specific data-set code
sequencingMethod	a string reporting the method used for the sequencing
sampleCondition	a string reporting the specific sample condition or time point
value	a value (or an array) containing the information
df	the data.frame
colName	the name of the new or existing column in the data.frame
colToSet	the column to add
rowNames	when not empty, if the input data.frame has no real row names, the new row names of the resulting data.frame

Details

getMetadataDataset() extracts the meta-data stored for the current data-set.

getMetadataElement() extracts the value associated with the given tag if present or an empty string otherwise.

getMetadataGenes() extracts the meta-data stored for the genes

getMetadataCells() extracts the meta-data stored for the cells

getDims() extracts the sizes of all slots of the COTAN object

datasetTags() defines a list of short names associated to an enumeration. It also defines the relative long names as they appear in the meta-data

initializeMetaDataset() initializes meta-data data-set

addElementToMetaDataset() is used to add a line of information to the meta-data data.frame. If the tag was already used it will update the associated value(s) instead

getColumnFromDF() is a function to extract a column from a data.frame, while keeping the rowNames as vector names

setColumnInDF() is a function to append, if missing, or resets, if present, a column into a data.frame, whether the data.frame is empty or not. The given rowNames are used only in the case the data.frame has only the default row numbers, so this function cannot be used to override row names

Value

getMetadataDataset() returns the meta-data data.frame

getMetadataElement() returns a string with the relevant value

getMetadataGenes() returns the genes' meta-data data.frame

getMetadataCells() returns the cells' meta-data data.frame

getDims() returns a named list with the sizes of the slots

datasetTags() a named ⁠character array⁠ with the standard labels used in the metaDataset of the COTAN objects

initializeMetaDataset() returns the given COTAN object with the updated metaDataset

addElementToMetaDataset() returns the updated COTAN object

getColumnFromDF() returns the column in the data.frame as named array, NULL if the wanted column is not available

setColumnInDF() returns the updated, or the newly created, data.frame

Examples

data("test.dataset")
objCOTAN <- COTAN(raw = test.dataset)

objCOTAN <- initializeMetaDataset(objCOTAN, GEO = "test_GEO",
                                  sequencingMethod = "distribution_sampling",
                                  sampleCondition = "reconstructed_dataset")

objCOTAN <- addElementToMetaDataset(objCOTAN, "Test",
                                    c("These are ", "some values"))

dataSetInfo <- getMetadataDataset(objCOTAN)

numInitialCells <- getMetadataElement(objCOTAN, "cells")

metaGenes <- getMetadataGenes(objCOTAN)

metaCells <- getMetadataCells(objCOTAN)

allSizes <- getDims(objCOTAN)

seriph78/COTAN documentation built on Dec. 10, 2024, 3:30 a.m.