calcSignalRange: Calculate a score range for multiple signals

In PhanstielLab/plotgardener: Coordinate-Based Genomic Visualization Package for R

Calculate a score range for multiple signals

Description

Calculate a score range for multiple signals

Usage

calcSignalRange(
    data,
    chrom = NULL,
    chromstart = 1,
    chromend = .Machine$integer.max,
    assembly = "hg38",
    negData = FALSE)

Arguments

data	List of data to be plotted as character values specifying multiple bigwig file paths, dataframes in BED format, or GRanges objects with metadata column score.
chrom	Chromosome of data region ragne as a string, if range for a specific chromosome is desired.
chromstart	Integer start position on chromosome to get data range.
chromend	Integer end position on chromosome to get data range.
assembly	Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
negData	A logical value indicating whether any of the data has both positive and negative scores and the signal range should be adjusted accordingly. Default value is negData = FALSE.

Value

Returns a vector of length 2 with the calculated c(min, max) range.

Examples

library("plotgardenerData")
data("GM12878_ChIP_CTCF_signal")
data("IMR90_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
data("IMR90_ChIP_H3K27ac_signal")

calcSignalRange(data = list(GM12878_ChIP_CTCF_signal, 
                            GM12878_ChIP_H3K27ac_signal, 
                            IMR90_ChIP_CTCF_signal, 
                            IMR90_ChIP_H3K27ac_signal),
                chrom = "chr21",
                chromstart = 28150000, chromend = 29150000,
                assembly = "hg38", negData = FALSE)

PhanstielLab/plotgardener documentation built on July 1, 2024, 7:06 p.m.