UniformTranscriptCheckers: Definition of the *Transcript Uniformity Checker* classes

In seriph78/COTAN: COexpression Tables ANalysis

Definition of the Transcript Uniformity Checker classes

Description

A hierarchy of classes to specify the method for checking whether a cluster has the Uniform Transcript property. It also doubles as result object.

getCheckerThreshold() extracts the main GDI threshold from the given checker object

calculateThresholdShiftToUniformity() calculates by how much the GDI thresholds in the given checker must be increased in order to have that the relevant cluster is deemed uniform transcript

shiftCheckerThresholds() returns a new checker object where the GDI thresholds where increased in order to relax the conditions to achieve uniform transcript

Usage

## S4 method for signature 'SimpleGDIUniformityCheck'
checkObjIsUniform(currentC, previousC = NULL, objCOTAN = NULL)

## S4 method for signature 'AdvancedGDIUniformityCheck'
checkObjIsUniform(currentC, previousC = NULL, objCOTAN = NULL)

checkersToDF(checkers)

dfToCheckers(df, checkerClass)

## S4 method for signature 'SimpleGDIUniformityCheck'
getCheckerThreshold(checker)

## S4 method for signature 'AdvancedGDIUniformityCheck'
getCheckerThreshold(checker)

## S4 method for signature 'SimpleGDIUniformityCheck'
calculateThresholdShiftToUniformity(checker)

## S4 method for signature 'AdvancedGDIUniformityCheck'
calculateThresholdShiftToUniformity(checker)

## S4 method for signature 'SimpleGDIUniformityCheck,numeric'
shiftCheckerThresholds(checker, shift)

## S4 method for signature 'AdvancedGDIUniformityCheck,numeric'
shiftCheckerThresholds(checker, shift)

Arguments

currentC	the object that defines the method and the threshold to discriminate whether a cluster is uniform transcript.
previousC	the optional result object of an already done check
objCOTAN	an optional COTAN object
checkers	a list of objects that defines the method, the thresholds and the results of the checks to discriminate whether a cluster is deemed uniform transcript.
df	a data.frame with col-names being the member names and row-names the names attached to each checker
checkerClass	the type of the checker to be reconstructed from the given data.frame
checker	An checker object that defines how to check for uniform transcript. It is derived from BaseUniformityCheck
shift	The amount by which to shift the GDI thresholds in the checker

Details

BaseUniformityCheck is the base class of the check methods

GDICheck represents a single unit check using GDI data. It defaults to an above check with threshold 1.4 and ratio 1\%

SimpleGDIUniformityCheck represents the simplified (and legacy) mechanism to determine whether a cluster has the Uniform Transcript property

The method is based on checking whether the fraction of the genes' GDI below the given threshold is less than the given ratio

AdvancedGDIUniformityCheck represents the more precise and advanced mechanism to determine whether a cluster has the Uniform Transcript property

The method is based on checking the genes' GDI against three thresholds: if a cluster fails the first below check is deemed not uniform. Otherwise if it passes either of the other two checks (one above and one below) it is deemed uniform.

checkObjIsUniform() performs the check whether the given object is uniform according to the given checker

checkersToDF() converts a list of checkers (i.e. objects that derive from BaseUniformityCheck) into a data.frame with the values of the members

dfToCheckers() converts a data.frame of checkers values into an array of checkers ensuring given data.frame is compatible with member types

Value

a copy of currentC with the results of the check. Note that the slot clusterSize will be set to zero if it is not possible to get the result of the check

a data.frame with col-names being the member names and row-names the names attached to each checker

dfToCheckers() returns a list of checkers of the requested type, each created from one of data.frame rows

getCheckerThreshold() returns the appropriate member of the checker object representing the main GDI threshold

calculateThresholdShiftToUniformity() returns the positive shift that would make the ⁠@isUniform⁠ slot TRUE in the checker. It returns zero if the result is already TRUE and NaN in case no such shift can exist (e.g. the check have been not done yet)

shiftCheckerThresholds() returns a copy of the checker object where all GDI thresholds have been shifted by the same given shift amount

Slots

isUniform

Logical. Output. The result of the check

clusterSize

Integer. Output. The number of cells in the checked cluster. When zero implies no check has been run yet

isCheckAbove

Logical. Determines how to compare quantiles against given thresholds. It is deemed passed if the relevant quantile is above/below the given threshold

GDIThreshold

Numeric. The level of GDI beyond which the cluster is deemed not uniform. Defaults

maxRatioBeyond

Numeric. The maximum fraction of the empirical GDI distribution that sits beyond the GDI threshold

maxRankBeyond

Integer. The minimum rank in the empirical GDI distribution for the GDI threshold

fractionBeyond

Numeric. Output. The fraction of genes whose GDI is above the threshold

thresholdRank

Integer. Output. The rank that the GDI threshold would have in the genes' GDI vector

quantileAtRatio

Numeric. Output. The quantile in the genes' GDI corresponding at the given ratio

quantileAtRatio

Numeric. Output. The quantile in the genes' GDI corresponding at the given rank

check

GDICheck. The single threshold check used to determine whether the cluster is deemed not uniform. Threshold defaults to 1.4, maxRatioBeyond to 1\%

firstCheck

GDICheck. Single threshold below check used to determine whether the cluster is deemed not uniform. Threshold defaults to 1.297, maxRatioBeyond to 5\%

secondCheck

GDICheck. Single threshold above check used to determine whether the cluster is deemed uniform. Threshold defaults to 1.307, maxRatioBeyond to 2\%

thirdCheck

GDICheck. Single threshold below check used to determine whether the cluster is deemed uniform. Threshold defaults to 1.4, maxRatioBeyond to 1\%

fourthCheck

GDICheck. Single threshold below check used to determine whether the cluster is deemed uniform. Threshold defaults to 1.4, maxRankBeyond to 2

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