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