getPlot: Graphical view of different ERs set for each Chip-seq...

In julaiti/MSPC: Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks

Description

This function is served as graphical version of export_ERs. To help user gaining deeper insight and biological evaluation of analysis result, using ggplot to generate stack bar plot for each Chip-seq replicates can be done.

Usage

getPlot(peakList_A, peakList_B, tau.s = 1e-08)

Arguments

peakList_A	output of runMSPC, is set of all confirmed ERs in GRanges objects.
peakList_B	output of runMSPC, is set of all discarded ERs in GRanges objects.
tau.s	permissive threshold for stringent enriched regions, all enriched regions below this threshold, are considered stringent ERs

Value

using ggplot to generate stack bar plot for file bar

Author(s)

Jurat Shahidin

Examples

# set up
library(GenomicRanges)
library(rtracklayer)

# load peak files
files <- getPeakFile()[1:3]
grs <- readPeakFiles(files, pvalueBase=1L)

## Exclude background noise
total.ERs <- denoise_ERs(peakGRs = grs, tau.w = 1.0E-04,
                        overwrite = TRUE)

## explore set of confirmed, discarde peaks
confirmedERs <- runMSPC(peakset = total.ERs, whichType = "max",
                        cmbStrgThreshold = 1.0E-08, isConfirmed = TRUE)
discardedERs <- runMSPC(peakset = total.ERs, whichType = "max",
                        cmbStrgThreshold = 1.0E-08, isConfirmed = FALSE)

# Visualize the output set for file bar
getPlot(peakList_A = confirmedERs,
        peakList_B = discardedERs, tau.s = 1.0E-08)

julaiti/MSPC documentation built on Oct. 17, 2019, 9:44 p.m.