plotCpGsite: Generate a plot of the model and raw data at one or more CpG...

In GarrettJenkinson/borealis: Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

Generate a plot of the model and raw data at one or more CpG sites

Description

Generate plots of model and results. The top panel of the plot will be the beta distribution in the beta-binomial model estimated for the cohort. The bottom panel will be the 95 percent confidence intervals around the percent methylation in each sample at that CpG site.

Usage

plotCpGsite(cpgSites, sampleOfInterest=NA, modelFile="CpG_model.csv",
                methCountFile="CpG_model_rawMethCount.tsv",
                totalCountFile="CpG_model_rawTotalCount.tsv")

Arguments

cpgSites	A character vector of CpG sites specified as "chr1:71732" representing the chromosome and start position of the CpG site. A separate plot will be generated for each site specified.
sampleOfInterest	(optional) character(1) Name of sample of interest which will be colored differently than the rest of the samples in the cohort. If NA then all samples will be plotted with same color.
modelFile	character(1) The mode file (including full path if not current working directory) with beta-binomial parameter estimates produced by runBorealis.
methCountFile	character(1) File name (including full path if not current working directory) for the methylated count file produced by runBorealis.
totalCountFile	character(1) File name (including full path if not current working directory) for the total count file produced by runBorealis.

Value

Returns a list with each element indexed by the provided cpgSites and storing a ggplot/cowplot object.

Examples

extdata <- system.file("extdata", package="borealis")
plots <- plotCpGsite("chr14:24780288",
        sampleOfInterest="patient_72",
        modelFile=file.path(extdata,"CpG_model_chr14.csv"),
        methCountFile=file.path(extdata,"CpG_model_rawMethCount_chr14.tsv"),
        totalCountFile=file.path(extdata,"CpG_model_rawTotalCount_chr14.tsv"))

GarrettJenkinson/borealis documentation built on Jan. 1, 2023, 6:16 a.m.