Man pages for BiSeq
Processing and analyzing bisulfite sequencing data
| 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... |
