The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
|Author||Katja Hebestreit, Hans-Ulrich Klein|
|Date of publication||None|
|Maintainer||Katja Hebestreit <firstname.lastname@example.org>|
annotateGRanges: Annotates a 'GRanges' object by means of a second 'GRanges'...
betaRegression: A function to estimate and test a group factor within a beta...
betaResults: The output of 'betaRegression'
betaResultsNull: The output of 'betaRegression' for resampled data
binomLikelihoodSmooth: Calculates local likelihood estimations for binomial random...
BSraw-class: Class to contain raw Bisulfite Sequencing (BiSeq) Data
BSrel-class: Class to contain Bisulfite Sequencing (BiSeq) Data
clusterSites: Assigns CpG cluster memberships on CpG sites within 'BSraw'...
clusterSitesToGR: A function to obtain a 'GRanges' object of CpG clusters from...
compareTwoSamples: Detects DMRs by comparing two samples
covBoxplots: Creates boxplots of coverages per sample
covStatistics: Prints a short summary of coverage statistics per sample
DMRs: The output of 'findDMRs'
estLocCor: Estimates the correlations of the z-scores
filterByCov: Filters regions (or single CpGs) of a 'BSraw' object with a...
filterBySharedRegions: Reduces a 'BSraw' or 'BSrel' object to regions (or single...
findDMRs: Aggregates CpG sites to DMRs
globalTest: Test whether at least one CpG is differentially methylated in...
limitCov: Limits the coverage of a 'BSraw' object
logisticRegression: Estimates and tests a group factor
makeVariogram: Variogram estimator.
plotBindingSites: Plots the mean methylation of given regions
plotMeth: Plots raw and smoothed methylation data for a given region
plotMethMap: Plots methylation values of multiple samples in a given...
plotSmoothMeth: Plots smoothed methylation values for a bunch of samples and...
predictedMeth: The output of 'predictMeth'
predictMeth: Predicts methylation levels along CpG sites or for a grid of...
promoters: A 'GRanges' of promoters of the human genome
rawToRel: Converts a 'BSraw' object to a 'BSrel' object
readBismark: Reads cytosine methylation stati determined by Bismark
rrbs: RRBS data of APL patient samples and controls.
smoothVariogram: Smoothes variogram
summarizeRegions: Aggregates methylation information of single CpG sites
testClusters: Tests CpG clusters
trimClusters: Trims CpG clusters
vario: Output of 'makeVariogram'
writeBED: Writes 'BSraw' and 'BSrel' data to a bed file suitable for...