Man pages for hansenlab/bsseq
Analyze, manage and store whole-genome methylation data
| BS.chr22 | Whole-genome bisulfite sequencing for chromosome 22 from... |
| BSmooth | BSmooth, smoothing bisulfite sequence data |
| BSmooth.fstat | Compute F-statistics based on smoothed whole-genome bisulfite... |
| BSmooth.tstat | Compute t-statistics based on smoothed whole-genome bisulfite... |
| BSseq | The constructor function for BSseq objects. |
| BSseq-class | Class BSseq |
| BSseqStat-class | Class BSseqStat |
| BSseqTstat-class | Class BSseqTstat |
| computeStat | Compute a test statistic based on smoothed whole-genome... |
| data.frame2GRanges | Converts a data frame to a GRanges. |
| dmrFinder | Finds differentially methylated regions for whole genome... |
| estimateErrorRate | Estimate CpG-specific error rate from BSseq object. |
| findLoci | Find methylation loci in a genome |
| fisherTests | Compute Fisher-tests for a BSseq object |
| FWGRanges-class | Classes FWIRanges and FWGRanges |
| getCoverage | Obtain coverage for BSseq objects. |
| getCpGMatrix | Generate a matrix of the most likely CpG status for a... |
| getCpGs | Get CpG (and non-CpG) loci from a single sample BSseq object. |
| getMaxLikelihoodMatrix | Generate a matrix of the scaled likelihood of most likely CpG... |
| getMeth | Obtain methylation estimates for BSseq objects. |
| getStats | Obtain statistics from a BSseqTstat object |
| goodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq... |
| hasGRanges-class | Class hasGRanges |
| internals | Internals |
| plotRegion | Plotting BSmooth methylation estimates |
| read.bedMethyl | Parsing bedMethyl output from modkit pileup. |
| read.bismark | Parsing output from the Bismark alignment suite. |
| read.modbam2bed | Construct BSseq objects from nanopore BED files |
| read.modkit | Construct BSseq objects from nanopore BED files |
| smoothSds | Smooth the standard deviations using a thresholded running... |
