Man pages for Bioconductor-mirror/BiSeq
Processing and analyzing bisulfite sequencing data

annotateGRangesAnnotates a 'GRanges' object by means of a second 'GRanges'...
betaRegressionA function to estimate and test a group factor within a beta...
betaResultsThe output of 'betaRegression'
betaResultsNullThe output of 'betaRegression' for resampled data
binomLikelihoodSmoothCalculates local likelihood estimations for binomial random...
BSraw-classClass to contain raw Bisulfite Sequencing (BiSeq) Data
BSrel-classClass to contain Bisulfite Sequencing (BiSeq) Data
clusterSitesAssigns CpG cluster memberships on CpG sites within 'BSraw'...
clusterSitesToGRA function to obtain a 'GRanges' object of CpG clusters from...
compareTwoSamplesDetects DMRs by comparing two samples
covBoxplotsCreates boxplots of coverages per sample
covStatisticsPrints a short summary of coverage statistics per sample
DMRsThe output of 'findDMRs'
estLocCorEstimates the correlations of the z-scores
filterByCovFilters regions (or single CpGs) of a 'BSraw' object with a...
filterBySharedRegionsReduces a 'BSraw' or 'BSrel' object to regions (or single...
findDMRsAggregates CpG sites to DMRs
globalTestTest whether at least one CpG is differentially methylated in...
limitCovLimits the coverage of a 'BSraw' object
logisticRegressionEstimates and tests a group factor
makeVariogramVariogram estimator.
plotBindingSitesPlots the mean methylation of given regions
plotMethPlots raw and smoothed methylation data for a given region
plotMethMapPlots methylation values of multiple samples in a given...
plotSmoothMethPlots smoothed methylation values for a bunch of samples and...
predictedMethThe output of 'predictMeth'
predictMethPredicts methylation levels along CpG sites or for a grid of...
promotersA 'GRanges' of promoters of the human genome
rawToRelConverts a 'BSraw' object to a 'BSrel' object
readBismarkReads cytosine methylation stati determined by Bismark
rrbsRRBS data of APL patient samples and controls.
smoothVariogramSmoothes variogram
summarizeRegionsAggregates methylation information of single CpG sites
testClustersTests CpG clusters
trimClustersTrims CpG clusters
varioOutput of 'makeVariogram'
writeBEDWrites 'BSraw' and 'BSrel' data to a bed file suitable for...
Bioconductor-mirror/BiSeq documentation built on July 1, 2017, 4:08 a.m.