{ "_id": "6a1b0a611d7bb097a0a06366", "Package": "sesame", "Type": "Package", "Title": "SEnsible Step-wise Analysis of DNA MEthylation BeadChips", "Description": "Tools For analyzing Illumina Infinium DNA methylation\narrays. SeSAMe provides utilities to support analyses of\nmultiple generations of Infinium DNA methylation BeadChips,\nincluding preprocessing, quality control, visualization and\ninference. SeSAMe features accurate detection calling,\nintelligent inference of ethnicity, sex and advanced quality\ncontrol routines.", "Version": "1.31.0", "Authors@R": "c(person(\"Wanding\", \"Zhou\", role = c(\"aut\",\"cre\",\"fnd\"), email = \"zhouwanding@gmail.com\", comment = c(ORCID = \"0000-0001-9126-1932\")),\nperson(\"Wubin\", \"Ding\", role = \"ctb\"),\nperson(\"David\", \"Goldberg\", role = \"ctb\"),\nperson(\"Ethan\", \"Moyer\", role = \"ctb\"),\nperson(\"Bret\", \"Barnes\", role = \"ctb\"),\nperson(\"Timothy\", \"Triche\", role = \"ctb\"),\nperson(\"Hui\", \"Shen\", role = c(\"aut\",\"fnd\"), email = \"Hui.Shen@vai.org\"))", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "URL": "https://github.com/zwdzwd/sesame", "BugReports": "https://github.com/zwdzwd/sesame/issues", "biocViews": "DNAMethylation, MethylationArray, Preprocessing,\nQualityControl", "Collate": "'readIDAT.R' 'sex.R' 'species.R' 'QC.R' 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"calcEffectSize" ] }, { "page": "checkLevels", "title": "filter data matrix by factor completeness only works for discrete factors", "topics": [ "checkLevels" ] }, { "page": "chipAddressToSignal", "title": "Lookup address in one sample", "topics": [ "chipAddressToSignal" ] }, { "page": "cnSegmentation", "title": "Perform copy number segmentation", "topics": [ "cnSegmentation" ] }, { "page": "compareMouseStrainReference", "title": "Compare Strain SNPs with a reference panel", "topics": [ "compareMouseStrainReference" ] }, { "page": "compareReference", "title": "Compare array data with references (e.g., tissue, cell types)", "topics": [ "compareReference" ] }, { "page": "controls", "title": "get the controls attributes", "topics": [ "controls" ] }, { "page": "convertProbeID", "title": "Convert Probe ID", "topics": [ "convertProbeID" ] }, { "page": "createUCSCtrack", "title": "Turn beta values into a UCSC browser track", "topics": [ "createUCSCtrack" ] }, { "page": "dataFrame2sesameQC", "title": "Convert data frame to sesameQC object", "topics": [ "dataFrame2sesameQC" ] }, { "page": "deIdentify", "title": "De-identify IDATs by removing SNP probes", "topics": [ "deIdentify" ] }, { "page": "detectionPnegEcdf", "title": "Detection P-value based on ECDF of negative control", "topics": [ "detectionPnegEcdf" ] }, { "page": "diffRefSet", "title": "Restrict refset to differentially methylated probes use with care, might introduce bias", "topics": [ "diffRefSet" ] }, { "page": "dmContrasts", "title": "List all contrasts of a DMLSummary", "topics": [ "dmContrasts" ] }, { "page": "DML", "title": "Test differential methylation on each locus", "topics": [ "DML" ] }, { "page": "DMLpredict", "title": "Predict new data from DML", "topics": [ "DMLpredict" ] }, { "page": "DMR", "title": "Find Differentially Methylated Region (DMR)", "topics": [ "DMR" ] }, { "page": "dyeBiasCorr", "title": "Correct dye bias in by linear scaling.", "topics": [ "dyeBiasCorr" ] }, { "page": "dyeBiasCorrMostBalanced", "title": "Correct dye bias using most balanced sample as the reference", "topics": [ "dyeBiasCorrMostBalanced" ] }, { "page": "dyeBiasL", "title": "Correct dye bias in by linear scaling.", "topics": [ "dyeBiasL" ] }, { "page": "dyeBiasNL", "title": "Dye bias correction by matching green and red to mid point", "topics": [ "dyeBiasCorrTypeINorm", "dyeBiasNL" ] }, { "page": "ELBAR", "title": "ELiminate BAckground-dominated Reading (ELBAR)", "topics": [ "ELBAR" ] }, { "page": "estimateLeukocyte", "title": "Estimate leukocyte fraction using a two-component model", "topics": [ "estimateLeukocyte" ] }, { "page": "formatVCF", "title": "Convert SNP from Infinium array to VCF file", "topics": [ "formatVCF" ] }, { "page": "getAFs", "title": "Get allele frequency", "topics": [ "getAFs" ] }, { "page": "getAFTypeIbySumAlleles", "title": "Get allele frequency treating type I by summing alleles", "topics": [ "getAFTypeIbySumAlleles" ] }, { "page": "getBetas", "title": "Get beta Values", "topics": [ "getBetas" ] }, { "page": "getBinCoordinates", "title": "Get bin coordinates", "topics": [ "getBinCoordinates" ] }, { "page": "getMask", "title": "get probe masking by mask names", "topics": [ "getMask" ] }, { "page": "getRefSet", "title": "Retrieve reference set", "topics": [ "getRefSet" ] }, { "page": "imputeBetas", "title": "Impute of missing data of specific platform", "topics": [ "imputeBetas" ] }, { "page": "imputeBetasByGenomicNeighbors", "title": "Impute missing data based on genomic neighbors.", "topics": [ "imputeBetasByGenomicNeighbors" ] }, { "page": "imputeBetasMatrixByMean", "title": "Impute Missing Values with Mean This function replaces missing values (NA) in a matrix, default is row means.", "topics": [ "imputeBetasMatrixByMean" ] }, { "page": "inferInfiniumIChannel", "title": "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.", "topics": [ "inferInfiniumIChannel" ] }, { "page": "inferSex", "title": "Infer sex.", "topics": [ "inferSex" ] }, { "page": "inferSpecies", "title": "Infer Species", "topics": [ "inferSpecies" ] }, { "page": "inferStrain", "title": "Infer strain information for mouse array", "topics": [ "inferStrain" ] }, { "page": "inferTissue", "title": "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.", "topics": [ "inferTissue" ] }, { "page": "initFileSet", "title": "initialize a fileSet class by allocating appropriate storage", "topics": [ "initFileSet" ] }, { "page": "listAvailableMasks", "title": "list existing quality masks for a SigDF", "topics": [ "listAvailableMasks" ] }, { "page": "mapFileSet", "title": "Deposit data of one sample to a fileSet (and hence to file)", "topics": [ "mapFileSet" ] }, { "page": "mapToMammal40", "title": "Map the SDF (from overlap array platforms) Replicates are merged by picking the best detection", "topics": [ "mapToMammal40" ] }, { "page": "matchDesign", "title": "normalize Infinium I probe betas to Infinium II", "topics": [ "matchDesign" ] }, { "page": "meanIntensity", "title": "Whole-dataset-wide Mean Intensity", "topics": [ "meanIntensity" ] }, { "page": "medianTotalIntensity", "title": "Whole-dataset-wide Median Total Intensity (M+U)", "topics": [ "medianTotalIntensity" ] }, { "page": "mLiftOver", "title": "Lift over beta values or SigDFs to another Infinium platform This function wraps ID conversion and provide optional imputation functionality.", "topics": [ "mLiftOver" ] }, { "page": "MValueToBetaValue", "title": "Convert M-value to beta-value", "topics": [ "MValueToBetaValue" ] }, { "page": "negControls", "title": "get negative control signal", "topics": [ "negControls" ] }, { "page": "noMasked", "title": "remove masked probes from SigDF", "topics": [ "noMasked" ] }, { "page": "noob", "title": "Noob background subtraction", "topics": [ "noob" ] }, { "page": "normControls", "title": "get normalization control signal", "topics": [ "normControls" ] }, { "page": "openSesame", "title": "The openSesame pipeline", "topics": [ "openSesame" ] }, { "page": "openSesameToFile", "title": "openSesame pipeline with file-backed storage", "topics": [ "openSesameToFile" ] }, { "page": "palgen", "title": "Generate some additional color palettes", "topics": [ "palgen" ] }, { "page": "parseGEOsignalMU", "title": "Convert signal M and U to SigDF", "topics": [ "parseGEOsignalMU" ] }, { "page": "pOOBAH", "title": "Detection P-value based on ECDF of out-of-band signal", "topics": [ "pOOBAH" ] }, { "page": "predictAge", "title": "Predict age using linear models", "topics": [ "predictAge" ] }, { "page": "prefixMask", "title": "Mask SigDF by probe ID prefix", "topics": [ "prefixMask" ] }, { "page": "prefixMaskButC", "title": "Mask all but C probes in SigDF", "topics": [ "prefixMaskButC" ] }, { "page": "prefixMaskButCG", "title": "Mask all but CG probes in SigDF", "topics": [ "prefixMaskButCG" ] }, { "page": "prepSesame", "title": "Apply a chain of sesame preprocessing functions in an arbitrary order", "topics": [ "prepSesame" ] }, { "page": "prepSesameList", "title": "List supported prepSesame functions", "topics": [ "prepSesameList" ] }, { "page": "print.DMLSummary", "title": "Print DMLSummary object", "topics": [ "print.DMLSummary" ] }, { "page": "print.fileSet", "title": "Print a fileSet", "topics": [ "print.fileSet" ] }, { "page": "probeID_designType", "title": "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", "topics": [ "probeID_designType" ] }, { "page": "probeSuccessRate", "title": "Whole-dataset-wide Probe Success Rate", "topics": [ "probeSuccessRate" ] }, { "page": "qualityMask", "title": "Mask beta values by design quality", "topics": [ "qualityMask" ] }, { "page": "readFileSet", "title": "Read an existing fileSet from storage", "topics": [ "readFileSet" ] }, { "page": "readIDATpair", "title": "Import a pair of IDATs from one sample", "topics": [ "readIDATpair" ] }, { "page": "recommendedMaskNames", "title": "Recommended mask names for each Infinium platform", "topics": [ "recommendedMaskNames" ] }, { "page": "reIdentify", "title": "Re-identify IDATs by restoring scrambled SNP intensities", "topics": [ "reIdentify" ] }, { "page": "resetMask", "title": "Reset Masking", "topics": [ "resetMask" ] }, { "page": "scrub", "title": "SCRUB background correction", "topics": [ "scrub" ] }, { "page": "scrubSoft", "title": "SCRUB background correction", "topics": [ "scrubSoft" ] }, { "page": "sdf_read_table", "title": "read a table file to SigDF", "topics": [ "sdf_read_table" ] }, { "page": "sdf_write_table", "title": "write SigDF to table file", "topics": [ "sdf_write_table" ] }, { "page": "SDFcollapseToPfx", "title": "collapse to probe prefix", "topics": [ "SDFcollapseToPfx" ] }, { "page": "sdfPlatform", "title": "Convenience function to output platform attribute of SigDF", "topics": [ "sdfPlatform" ] }, { "page": "searchIDATprefixes", "title": "Identify IDATs from a directory", "topics": [ "searchIDATprefixes" ] }, { "page": "segmentBins", "title": "Segment bins using DNAcopy", "topics": [ "segmentBins" ] }, { "page": "sesame_checkVersion", "title": "Check SeSAMe versions", "topics": [ "sesame_checkVersion" ] }, { "page": "sesameAnno_attachManifest", "title": "Annotate a data.frame using manifest", "topics": [ "sesameAnno_attachManifest" ] }, { "page": "sesameAnno_buildAddressFile", "title": "Build sesame ordering address file from tsv", "topics": [ "sesameAnno_buildAddressFile" ] }, { "page": "sesameAnno_buildManifestGRanges", "title": "Build manifest GRanges from tsv", "topics": [ "sesameAnno_buildManifestGRanges" ] }, { "page": "sesameAnno_download", "title": "Download SeSAMe annotation files", "topics": [ "sesameAnno_download" ] }, { "page": "sesameAnno_readManifestTSV", "title": "Read manifest file to a tsv format", "topics": [ "sesameAnno_readManifestTSV" ] }, { "page": "sesameQC_calcStats", "title": "Calculate QC statistics", "topics": [ "sesameQC_calcStats" ] }, { "page": "sesameQC_getStats", "title": "Get stat numbers from an sesameQC object", "topics": [ "sesameQC_getStats" ] }, { "page": "sesameQC_plotBar", "title": "Bar plots for sesameQC", "topics": [ "sesameQC_plotBar" ] }, { "page": "sesameQC_plotBetaByDesign", "title": "Plot betas distinguishing different Infinium chemistries", "topics": [ "sesameQC_plotBetaByDesign" ] }, { "page": "sesameQC_plotHeatSNPs", "title": "Plot SNP heatmap", "topics": [ "sesameQC_plotHeatSNPs" ] }, { "page": "sesameQC_plotIntensVsBetas", "title": "Plot Total Signal Intensities vs Beta Values This plot is helpful in revealing the extent of signal background and dye bias.", "topics": [ "sesameQC_plotIntensVsBetas" ] }, { "page": "sesameQC_plotRedGrnQQ", "title": "Plot red-green QQ-Plot using Infinium-I Probes", "topics": [ "sesameQC_plotRedGrnQQ" ] }, { "page": "sesameQC_rankStats", "title": "This function compares the input sample with public data. Only overlapping metrics will be compared.", "topics": [ "sesameQC_rankStats" ] }, { "page": "sesameQC-class", "title": "An S4 class to hold QC statistics", "topics": [ "sesameQC-class" ] }, { "page": "sesameQCtoDF", "title": "Convert a list of sesameQC to data frame", "topics": [ "sesameQCtoDF" ] }, { "page": "setMask", "title": "Set mask to only the probes specified", "topics": [ "setMask" ] }, { "page": "SigDF", "title": "SigDF validation from a plain data frame", "topics": [ "SigDF" ] }, { "page": "signalMU", "title": "report M and U for regular probes", "topics": [ "signalMU" ] }, { "page": "sliceFileSet", "title": "Slice a fileSet with samples and probes", "topics": [ "sliceFileSet" ] }, { "page": "summaryExtractTest", "title": "Extract slope information from DMLSummary", "topics": [ "summaryExtractTest" ] }, { "page": "totalIntensities", "title": "M+U Intensities Array", "topics": [ "totalIntensities" ] }, { "page": "twoCompsEst2", "title": "Estimate the fraction of the 2nd component in a 2-component mixture", "topics": [ "twoCompsEst2" ] }, { "page": "updateSigDF", "title": "Set color and mask using strain/species-specific manifest", "topics": [ "updateSigDF" ] }, { "page": "visualizeGene", "title": "Visualize Gene", "topics": [ "visualizeGene" ] }, { "page": "visualizeProbes", "title": "Visualize Region that Contains the Specified Probes", "topics": [ "visualizeProbes" ] }, { "page": "visualizeRegion", "title": "Visualize Region", "topics": [ "visualizeRegion" ] }, { "page": "visualizeSegments", "title": "Visualize segments", "topics": [ "visualizeSegments" ] } ], "_readme": "https://github.com/bioc/sesame/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocParallel", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "clipr", "codetools", "colorspace", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "ExperimentHub", "farver", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "plyr", "png", "preprocessCore", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "reshape2", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "sesameData", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "wheatmap", "withr", "XVector", "yaml" ], "_vignettes": [ { "source": "sesame.Rmd", "filename": "sesame.html", "title": "Basic Usage & Preprocessing", "engine": "knitr::rmarkdown", "headings": [ "Preparation", "The openSesame 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