singleRun: singleRun

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

singleRun

Description

singleRun runs ChIPanalyser after optimal paramters have been found by the evolve function.

Usage

  singleRun(indiv,DNAAffinity,
            genomicProfiles,DNASequenceSet,
            ChIPScore,fitness="all")

Arguments

indiv	Population list containing the top scoring individual. Note that this should be a list of length 1 containing another list with all parameter values.
DNAAffinity	GRanges object as outputed by the setchromatinStates.
genomicProfiles	genomicProfiles object containing PWM scores and other desired metrics. Note that PWMThreshold, lambda and N will be overwritten using values from indiv.
DNASequenceSet	DNA string set object containing DNA sequence of interest.
ChIPScore	ChIPScore object as outputed by the processingChIP function.
fitness	character string describing which metric should be used to assess fitness and should be one of the following:"geometric","ks","MSE","pearson","spearman","kendall", "recall","precesion","fscore","MCC","Accuracy" or "AUC".

Details

Once the genetic algorithm has been optimised, the top individual may be run on its own to get predicted ChIP profiles. The use of this function requires a few extract steps in order to predict ChIP profiles.

First, the index of the top individual should be extracted (see getHighestFitnessSolutions). Second, using this index, subset top individual from GA population. Note this should be done using "[]" single bracket notation as, a list of length 1 containing another list with all parameter values is required for the next steps. Yes, this is might seem annoying but the functions were design for list structures... Third, setchromatinStates using the top individual list. This will add chromatin affinity values to your chromatinState GRanges. Use this new chromatinState object as your new chromatinState object. Fourth, parse your indiv list object to singleRun.

Value

Return a list with three elements. First element contains a genomicProfiles object with occupancy scores. Second element contains a genomicProfiles objecy with ChIP profile scores. Third element contains a goodness of fit metrics.

Author(s)

Patrick C.N. Martin <[e-mail]

Examples

library(ChIPanalyser)
data(ChIPanalyserData)
# See GA vignette for usage 

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.