setChromatinStates: setChromatinStates

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

setChromatinStates

Description

setChromatinStates sets chromatin state affinity values to a GRanges object.

Usage

  setChromatinStates(population,chromatinStates)

Arguments

population	Population list containing all individuals and associated parameter. Must contain chromatin state affinity values. See generateStartingPopulation.
chromatinStates	GRanges object containing chromatin state locations.

Details

Chromatin states can be loaded into R as a GRanges object. Each range represents the extent of a certain chromatin state and the chromatin state type should be assigned to a meta data column called "name". The affinity values names should be set accordingly.

Value

Returns a GRange object with affinity scores for each chromatin state range. Affinity scores are placed in the DNAAffinity meta data column.

Author(s)

Patrick C.N. Martin

Examples

library(ChIPanalyser)
# Input data 
data(ChIPanalyserData)

pop <- 10
params <- c("N","lambda","PWMThreshold", paste0("CS",seq(1:11)))
start_pop <- generateStartingPopulation(pop, params)

cs <- setChromatinStates(start_pop,cs)

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