# SEnsible Step-wise Analysis of DNA MEthylation BeadChips

## Documentation for package ‘sesame’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I K L M N O P Q R S T U V misc

sesame-package | Analyze DNA methylation data

## -- A --

addMask | Add probes to mask
aggregateTestEnrichments | Aggregate test enrichment results
assemble_plots | assemble plots

## -- B --

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

## -- C --

calcEffectSize | Compute effect size for different variables from prediction matrix
checkLevels | filter data matrix by factor completeness only works for discrete factors
chipAddressToSignal | Lookup address in one sample
cnSegmentation | Perform copy number segmentation
compareDatbaseSetOverlap | calculates the pariwise overlap between given list of database sets using a distance metric.
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
convertTo | Convert human arrays to previous platforms Missing probes are replaced using NAs.
createDBNetwork | createGeneNetwork creates database network using the Jaccard index.
createUCSCtrack | Turn beta values into a UCSC browser track

## -- D --

dataFrame2sesameQC | Convert data frame to sesameQC object
dbStats | dbStats builds dataset for a given betas matrix composed of engineered features from the given database sets
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 care, might introduce bias
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
dyeBiasCorrTypeINorm | Dye bias correction by matching green and red to mid point
dyeBiasL | Correct dye bias in by linear scaling.
dyeBiasNL | Dye bias correction by matching green and red to mid point

## -- E --

ELBAR | ELiminate BAckground-dominated Reading (ELBAR)
estimateCellComposition | Estimate cell composition using reference
estimateLeukocyte | Estimate leukocyte fraction using a two-component model

## -- F --

formatVCF | Convert SNP from Infinium array to VCF file

## -- G --

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
getSexInfo | Get sex-related information

## -- I --

imputeTo | Impute to platform
inferEthnicity | Infer Ethnicity
inferInfiniumIChannel | 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.
inferSex | Infer Sex
inferSexKaryotypes | Infer Sex Karyotype
inferSpecies | Infer Species
inferStrain | Infer strain information for mouse array
inferTissue | 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.
initFileSet | initialize a fileSet class by allocating appropriate storage

## -- K --

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 group(s)
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 fields estimate.
KYCG_plotManhattan | KYCG_plotManhattan makes a manhattan plot to summarize EWAS results
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 against the same set of databases
KYCG_plotSetEnrichment | Plot Set Enrichment
KYCG_plotVolcano | creates a volcano plot of -log2(p.value) and log(estimate) given data with fields estimate and p.value.
KYCG_plotWaterfall | create a waterfall plot of log(estimate) given test enrichment

## -- L --

listAvailableMasks | list existing quality masks for a SigDF

## -- M --

mapFileSet | Deposit data of one sample to a fileSet (and hence to file)
mapToMammal40 | Map the SDF (from overlap array platforms) Replicates are merged by picking the best detection
matchDesign | normalize Infinium I probe betas to Infinium II
meanIntensity | Whole-dataset-wide Mean Intensity
medianTotalIntensity | Whole-dataset-wide Median Total Intensity (M+U)
MValueToBetaValue | Convert M-value to beta-value

## -- N --

negControls | get negative control signal
noMasked | remove masked probes from SigDF
noob | Noob background subtraction
normControls | get normalization control signal

## -- O --

openSesame | The openSesame pipeline
openSesameToFile | openSesame pipeline with file-backed storage

## -- P --

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 arbitrary order
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 with the new probe ID system. See https://github.com/zhou-lab/InfiniumAnnotation for illustration
probeSuccessRate | Whole-dataset-wide Probe Success Rate

## -- Q --

qualityMask | Mask beta values by design quality

## -- R --

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

## -- S --

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
sesame | Analyze DNA methylation data
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 repository
sesameAnno_readManifestTSV | Read manifest file to a tsv format
sesameData_getAnno | retrieve additional annotation files
sesameQC-class | An S4 class to hold QC statistics
sesameQC_calcStats | Calculate 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 helpful in revealing the extent of signal background and dye bias.
sesameQC_plotRedGrnQQ | Plot red-green QQ-Plot using Infinium-I Probes
sesameQC_rankStats | This function compares the input sample with public data. Only overlapping metrics will be compared.
sesame_checkVersion | Check SeSAMe versions
sesamize | sesamize function is deprecated. Please check https://github.com/zwdzwd/sesamize for previous scripts
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

## -- T --

testEnrichment | testEnrichment tests for the enrichment of set of probes (query set) in a number of features (database sets).
testEnrichmentFisher | testEnrichmentFisher uses Fisher's exact test to estimate the association between two categorical variables.
testEnrichmentGene | Convenient function for testing enrichment of gene linkage
testEnrichmentSEA | uses the GSEA-like test to estimate the association of a categorical variable against a continuous variable.
testEnrichmentSpearman | testEnrichmentSpearman uses the Spearman statistical test to estimate the association between two continuous variables.
totalIntensities | M+U Intensities Array
twoCompsEst2 | Estimate the fraction of the 2nd component in a 2-component mixture

## -- U --

updateSigDF | Set color and mask using strain/species-specific manifest

## -- V --

visualizeGene | Visualize Gene
visualizeProbes | Visualize Region that Contains the Specified Probes
visualizeRegion | Visualize Region
visualizeSegments | Visualize segments

## -- misc --

_PACKAGE | Analyze DNA methylation data