Man pages for zwdzwd/sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
| addMask | Add probes to mask |
| aggregateTestEnrichments | Aggregate test enrichment results |
| assemble_plots | assemble plots |
| betasCollapseToPfx | Collapse betas by averagng probes with common probe ID prefix |
| BetaValueToMValue | Convert beta-value to M-value |
| binSignals | Bin signals from probe signals |
| bisConversionControl | Compute internal bisulfite conversion control |
| calcEffectSize | Compute effect size for different variables from prediction... |
| checkLevels | filter data matrix by factor completeness only works for... |
| chipAddressToSignal | Lookup address in one sample |
| cnSegmentation | Perform copy number segmentation |
| compareDatbaseSetOverlap | calculates the pariwise overlap between given list of... |
| compareMouseStrainReference | Compare Strain SNPs with a reference panel |
| compareMouseTissueReference | Compare mouse array data with mouse tissue references |
| compareReference | Compare array data with references (e.g., tissue, cell types) |
| controls | get the controls attributes |
| convertProbeID | Convert Probe ID |
| createDBNetwork | createGeneNetwork creates database network using the Jaccard... |
| createUCSCtrack | Turn beta values into a UCSC browser track |
| dataFrame2sesameQC | Convert data frame to sesameQC object |
| dbStats | dbStats builds dataset for a given betas matrix composed of... |
| deidentify | De-identify IDATs by removing SNP probes |
| detectionPnegEcdf | Detection P-value based on ECDF of negative control |
| diffRefSet | Restrict refset to differentially methylated probes use with... |
| dmContrasts | List all contrasts of a DMLSummary |
| DML | Test differential methylation on each locus |
| DMLpredict | Predict new data from DML |
| DMR | Find Differentially Methylated Region (DMR) |
| dyeBiasCorr | Correct dye bias in by linear scaling. |
| dyeBiasCorrMostBalanced | Correct dye bias using most balanced sample as the reference |
| dyeBiasL | Correct dye bias in by linear scaling. |
| dyeBiasNL | Dye bias correction by matching green and red to mid point |
| ELBAR | ELiminate BAckground-dominated Reading (ELBAR) |
| estimateCellComposition | Estimate cell composition using reference |
| estimateLeukocyte | Estimate leukocyte fraction using a two-component model |
| formatVCF | Convert SNP from Infinium array to VCF file |
| getAFs | Get allele frequency |
| getAFTypeIbySumAlleles | Get allele frequency treating type I by summing alleles |
| getBetas | Get beta Values |
| getBinCoordinates | Get bin coordinates |
| getMask | get probe masking by mask names |
| getRefSet | Retrieve reference set |
| imputeBetas | Impute of missing data of specific platform |
| imputeBetasMatrixByMean | Impute Missing Values with Mean This function replaces... |
| inferEthnicity | Infer Ethnicity |
| inferInfiniumIChannel | Infer and reset color channel for Type-I probes instead of... |
| inferSex | Infer sex. |
| inferSpecies | Infer Species |
| inferStrain | Infer strain information for mouse array |
| inferTissue | inferTissue infers the tissue of a single sample (as... |
| initFileSet | initialize a fileSet class by allocating appropriate storage |
| KYCG_annoProbes | Annotate Probe IDs using KYCG databases |
| KYCG_buildGeneDBs | build gene-probe association database |
| KYCG_getDBs | Get databases by full or partial names of the database... |
| KYCG_listDBGroups | List database group names |
| KYCG_loadDBs | Load database groups |
| KYCG_plotBar | Bar plot to show most enriched CG groups from testEnrichment |
| KYCG_plotDot | Dot plot to show most enriched CG groups from testEnrichment |
| KYCG_plotEnrichAll | plot enrichment test result |
| KYCG_plotLollipop | creates a lollipop plot of log(estimate) given data with... |
| KYCG_plotManhattan | KYCG_plotManhattan makes a manhattan plot to summarize EWAS... |
| KYCG_plotMeta | Plot meta gene or other meta genomic features |
| KYCG_plotMetaEnrichment | Plot meta gene or other meta genomic features |
| KYCG_plotPointRange | Plot point range for a list of enrichment testing results... |
| KYCG_plotSetEnrichment | Plot Set Enrichment |
| KYCG_plotVolcano | creates a volcano plot of -log2(p.value) and log(estimate)... |
| KYCG_plotWaterfall | create a waterfall plot of log(estimate) given test... |
| liftOver | liftOver, see mLiftOver (renamed) |
| listAvailableMasks | list existing quality masks for a SigDF |
| mapFileSet | Deposit data of one sample to a fileSet (and hence to file) |
| mapToMammal40 | Map the SDF (from overlap array platforms) Replicates are... |
| matchDesign | normalize Infinium I probe betas to Infinium II |
| meanIntensity | Whole-dataset-wide Mean Intensity |
| medianTotalIntensity | Whole-dataset-wide Median Total Intensity (M+U) |
| mLiftOver | Lift over beta values or SigDFs to another Infinium platform... |
| MValueToBetaValue | Convert M-value to beta-value |
| negControls | get negative control signal |
| noMasked | remove masked probes from SigDF |
| noob | Noob background subtraction |
| normControls | get normalization control signal |
| openSesame | The openSesame pipeline |
| openSesameToFile | openSesame pipeline with file-backed storage |
| palgen | Generate some additional color palettes |
| parseGEOsignalMU | Convert signal M and U to SigDF |
| pOOBAH | Detection P-value based on ECDF of out-of-band signal |
| predictAge | Predict age using linear models |
| predictAgeHorvath353 | Horvath 353 age predictor |
| predictAgeSkinBlood | Horvath Skin and Blood age predictor |
| predictMouseAgeInMonth | Mouse age predictor |
| prefixMask | Mask SigDF by probe ID prefix |
| prefixMaskButC | Mask all but C probes in SigDF |
| prefixMaskButCG | Mask all but CG probes in SigDF |
| prepSesame | Apply a chain of sesame preprocessing functions in an... |
| prepSesameList | List supported prepSesame functions |
| print.DMLSummary | Print DMLSummary object |
| print.fileSet | Print a fileSet |
| probeID_designType | Extract the probe type field from probe ID This only works... |
| probeSuccessRate | Whole-dataset-wide Probe Success Rate |
| qualityMask | Mask beta values by design quality |
| readFileSet | Read an existing fileSet from storage |
| readIDATpair | Import a pair of IDATs from one sample |
| recommendedMaskNames | Recommended mask names for each Infinium platform |
| reIdentify | Re-identify IDATs by restoring scrambled SNP intensities |
| resetMask | Reset Masking |
| scrub | SCRUB background correction |
| scrubSoft | SCRUB background correction |
| SDFcollapseToPfx | collapse to probe prefix |
| sdfPlatform | Convenience function to output platform attribute of SigDF |
| sdf_read_table | read a table file to SigDF |
| sdf_write_table | write SigDF to table file |
| searchIDATprefixes | Identify IDATs from a directory |
| segmentBins | Segment bins using DNAcopy |
| sesameAnno_buildAddressFile | Build sesame ordering address file from tsv |
| sesameAnno_buildManifestGRanges | Build manifest GRanges from tsv |
| sesameAnno_download | Download SeSAMe annotation files |
| sesameAnno_get | download Infinium manifest from the associated Github... |
| sesameAnno_readManifestTSV | Read manifest file to a tsv format |
| sesame_checkVersion | Check SeSAMe versions |
| sesameData_getAnno | retrieve additional annotation files |
| sesame-package | Analyze DNA methylation data |
| sesameQC_calcStats | Calculate QC statistics |
| sesameQC-class | An S4 class to hold QC statistics |
| sesameQC_getStats | Get stat numbers from an sesameQC object |
| sesameQC_plotBar | Bar plots for sesameQC |
| sesameQC_plotBetaByDesign | Plot betas distinguishing different Infinium chemistries |
| sesameQC_plotHeatSNPs | Plot SNP heatmap |
| sesameQC_plotIntensVsBetas | Plot Total Signal Intensities vs Beta Values This plot is... |
| sesameQC_plotRedGrnQQ | Plot red-green QQ-Plot using Infinium-I Probes |
| sesameQC_rankStats | This function compares the input sample with public data.... |
| sesamize | sesamize function is deprecated. Please check... |
| setMask | Set mask to only the probes specified |
| SigDF | SigDF validation from a plain data frame |
| signalMU | report M and U for regular probes |
| sliceFileSet | Slice a fileSet with samples and probes |
| summaryExtractTest | Extract slope information from DMLSummary |
| testEnrichment | testEnrichment tests for the enrichment of set of probes... |
| testEnrichmentFisher | testEnrichmentFisher uses Fisher's exact test to estimate the... |
| testEnrichmentGene | Convenient function for testing enrichment of gene linkage |
| testEnrichmentSEA | uses the GSEA-like test to estimate the association of a... |
| testEnrichmentSpearman | testEnrichmentSpearman uses the Spearman statistical test to... |
| totalIntensities | M+U Intensities Array |
| twoCompsEst2 | Estimate the fraction of the 2nd component in a 2-component... |
| updateSigDF | Set color and mask using strain/species-specific manifest |
| visualizeGene | Visualize Gene |
| visualizeProbes | Visualize Region that Contains the Specified Probes |
| visualizeRegion | Visualize Region |
| visualizeSegments | Visualize segments |
