CorrelationLinkList: Generate a CorrelationLinkList

In VEuPathDB/plot.data: Create `data.table`s of Ready to Plot Data

Generate a CorrelationLinkList

Description

Generate a CorrelationLinkList from an edgeList

Usage

CorrelationLinkList(
  object,
  linkColorScheme = c("none", "posneg"),
  correlationCoefThreshold = NULL,
  pValueThreshold = NULL
)

## S4 method for signature 'data.frame'
CorrelationLinkList(
  object = data.frame(source = character(), target = character(), correlationCoef =
    numeric(), pValue = numeric()),
  linkColorScheme = c("none", "posneg"),
  correlationCoefThreshold = NULL,
  pValueThreshold = NULL
)

## S4 method for signature 'missing'
CorrelationLinkList(object)

## S4 method for signature 'SimpleList'
CorrelationLinkList(object)

## S4 method for signature 'list'
CorrelationLinkList(object)

Arguments

object	Object containing data to be converted to a LinkList. Could be a SimpleList of Links or a data.frame with columns source, target, correlationCoef, pValue.
linkColorScheme	Either 'none' or 'posneg'. If 'posneg', the link color will be based on the sign of the correlation coefficient.
correlationCoefThreshold	numeric value used to filter links based on correlationCoef. Default is NULL (i.e. no filtering). Any links with an absolute correlationCoef below this threshold will be removed.
pValueThreshold	numeric value used to filter links based on pValue. Default is NULL (i.e. no filtering). Any links with an pValue above this threshold will be removed.

Value

CorrelationLinkList

Examples

CorrelationLinkList(data.frame(source='a',target='b',correlationCoef=0.5,pValue=0.01))

VEuPathDB/plot.data documentation built on Feb. 20, 2025, 6:33 p.m.