HandlingConditions: Handling cells' _conditions_ and related functions

In seriph78/COTAN: COexpression Tables ANalysis

Handling cells' conditions and related functions

Description

These functions manage the conditions.

A condition is a set of labels that can be assigned to cells: one label per cell. This is especially useful in cases when the data-set is the result of merging multiple experiments' raw data

Usage

## S4 method for signature 'COTAN'
getAllConditions(objCOTAN, keepPrefix = FALSE)

## S4 method for signature 'COTAN'
getConditionName(objCOTAN, condName = "", keepPrefix = FALSE)

## S4 method for signature 'COTAN'
getCondition(objCOTAN, condName = "")

normalizeNameAndLabels(objCOTAN, name = "", labels = NULL, isCond = FALSE)

## S4 method for signature 'COTAN'
addCondition(objCOTAN, condName, conditions, override = FALSE)

## S4 method for signature 'COTAN'
dropCondition(objCOTAN, condName)

Arguments

objCOTAN	a COTAN object
keepPrefix	When TRUE returns the internal name of the condition: the one with the COND_ prefix.
condName	the name of an existing condition.
name	the name of the clusterization/condition. If not given the last available clusterization will be used, or no conditions
labels	a clusterization/condition to use. If given it will take precedence on the one indicated by name
isCond	a Boolean to indicate whether the function is dealing with clusterizations FALSE or conditions TRUE
conditions	a (factors) array of condition labels
override	When TRUE silently allows overriding data for an existing condition name. Otherwise the default behavior will avoid potential data losses

Details

getAllConditions() extracts the list of the conditions defined in the COTAN object.

getConditionName() normalizes the given condition name or, if none were given, returns the name of last available condition in the COTAN object. It can return the condition internal name if needed

getCondition() extracts the asked condition from the COTAN object

normalizeNameAndLabels() takes a pair of name/labels and normalize them based on the available information in the COTAN object

addCondition() adds a condition to the current COTAN object, by adding a new column in the metaCells data.frame

dropCondition() drops a condition from the current COTAN object, by removing the corresponding column in the metaCells data.frame

Value

getAllConditions() returns a vector of conditions names, usually without the COND_ prefix

getConditionName() returns the normalized condition name or NULL if no conditions are present

getCondition() returns a named factor with the condition

normalizeNameAndLabels() returns a list with:

• "name" the relevant name

• "labels" the relevant clusterization/condition

addCondition() returns the updated COTAN object

dropCondition() returns the updated COTAN object

Examples

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

cellLine <- rep(c("A", "B"), getNumCells(objCOTAN) / 2)
names(cellLine) <- getCells(objCOTAN)
objCOTAN <- addCondition(objCOTAN, condName = "Line", conditions = cellLine)

##objCOTAN <- dropCondition(objCOTAN, "Genre")

conditionsNames <- getAllConditions(objCOTAN)

condName <- getConditionName(objCOTAN)

condition <- getCondition(objCOTAN, condName = condName)
isa(condition, "factor")

nameAndCond <- normalizeNameAndLabels(objCOTAN, name = condName,
                                      isCond = TRUE)
isa(nameAndCond[["labels"]], "factor")

seriph78/COTAN documentation built on Nov. 15, 2024, 7:09 a.m.