{ "_id": "6aca1e47fe5cc25786e84de2", "Package": "ChAMPdata", "Type": "Package", "Title": "Data Packages for ChAMP package", "Version": "2.45.1", "Date": "2021-11-22", "Author": "Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling\n[ctb] and Andrew Teschendorff [ctb]", "Maintainer": "Yuan Tian ", "Description": "Provides datasets needed for ChAMP including a test\ndataset and blood controls for CNA analysis.", "License": "GPL-3", "biocViews": "ExperimentData", "PackageStatus": "Deprecated", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-09-14 15:18:56 UTC", "RemoteUrl": "https://git.bioconductor.org/packages/ChAMPdata", "RemoteRef": "HEAD", "RemoteSha": "5eb766f3651df6e06e498c80790a793393e6c25c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 10:40:28 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "ChAMPdata_2.45.1.tar.gz", "_fileid": "https://r2.ropensci.org/117ff888a50516301cd3336df138ab3e674ab1186acf9795b842b8cfd5e2f190", "_filesize": 517481929, "_sha256": "117ff888a50516301cd3336df138ab3e674ab1186acf9795b842b8cfd5e2f190", "_expires": "2027-01-18T11:14:48.000Z", "_created": "2026-10-10T10:40:28.000Z", "_published": "2026-10-10T11:15:19.258Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38045093705", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 6, "warning": 6, "note": 7 }, "_upstream": "https://git.bioconductor.org/packages/ChAMPdata", "_commit": { "id": "5eb766f3651df6e06e498c80790a793393e6c25c", "author": "lshep ", "committer": "lshep ", "message": "unresponsive\n\n- large files\n", "time": 1789399136 }, "_maintainer": { "name": "Yuan Tian", "email": "champ450k@gmail.com" }, "_distro": "resolute", "_jobs": [ { "job": 114198909254, "time": 134, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11668191314" }, { "job": 114198909243, "time": 517, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11668845456" }, { "job": 114198909273, "time": 408, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11668146813" }, { "job": 114192973082, "time": 2100, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11667816439" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.22.4", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.16.1", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-38", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.45.1", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "2.44.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimentdata", "datapkg" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 52, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/ChAMPdata.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "bloodCtl", "title": "Blood Control data", "object": "champBloodCtls", "file": "champBloodCtls.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "CellTypeMeans27K", "title": "Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.", "object": "CellTypeMeans27K", "file": "CellTypeMeans27K.rda", "class": [ "matrix", "array" ], "fields": [ "CD8T", "CD4T", "NK", "Bcell", "Mono", "Gran" ], "rows": 500, "table": true, "tojson": true }, { "name": "CellTypeMeans450K", "title": "Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.", "object": "CellTypeMeans450K", "file": "CellTypeMeans450K.rda", "class": [ "matrix", "array" ], "fields": [ "CD8T", "CD4T", "NK", "Bcell", "Mono", "Gran" ], "rows": 600, "table": true, "tojson": true }, { "name": "EPIC.manifest.hg19", "title": "SNP annotation for EPIC array.", "object": "EPIC.manifest.hg19", "file": "EPIC.manifest.hg19.rda", "class": [ "data.frame" ], "fields": [ "CpG_chrm", "CpG_beg", "CpG_end", "probe_strand", "probeID", "address_A", "address_B", "channel", "designType", "nextBase", "nextBaseRef", "probeType", "orientation", "probeCpGcnt", "context35", "probeBeg", "probeEnd", "ProbeSeq_A", "ProbeSeq_B", "gene", "gene_HGNC", "chrm_A", "beg_A", "flag_A", "mapQ_A", "cigar_A", "NM_A", "chrm_B", "beg_B", "flag_B", "mapQ_B", "cigar_B", "NM_B", "wDecoy_chrm_A", "wDecoy_beg_A", "wDecoy_flag_A", "wDecoy_mapQ_A", "wDecoy_cigar_A", "wDecoy_NM_A", "wDecoy_chrm_B", "wDecoy_beg_B", "wDecoy_flag_B", "wDecoy_mapQ_B", "wDecoy_cigar_B", "wDecoy_NM_B", "posMatch", "MASK_mapping", "MASK_typeINextBaseSwitch", "MASK_rmsk15", "MASK_sub40_copy", "MASK_sub35_copy", "MASK_sub30_copy", "MASK_sub25_copy", "MASK_snp5_common", "MASK_snp5_GMAF1p", "MASK_extBase", "MASK_general" ], "rows": 865918, "table": true, "tojson": true }, { "name": "EPIC.manifest.pop.hg19", "title": "SNP annotation for EPIC array for different population.", "object": "EPIC.manifest.pop.hg19", "file": "EPIC.manifest.pop.hg19.rda", "class": [ "data.frame" ], "fields": [ "CpG_chrm", "CpG_beg", "CpG_end", "probeID", "MASK_general_AFR", "MASK_snp5_AFR", "MASK_general_EAS", "MASK_snp5_EAS", "MASK_general_EUR", "MASK_snp5_EUR", "MASK_general_SAS", "MASK_snp5_SAS", "MASK_general_AMR", "MASK_snp5_AMR", "MASK_general_GWD", "MASK_snp5_GWD", "MASK_general_YRI", "MASK_snp5_YRI", "MASK_general_TSI", "MASK_snp5_TSI", "MASK_general_IBS", "MASK_snp5_IBS", "MASK_general_CHS", "MASK_snp5_CHS", "MASK_general_PUR", "MASK_snp5_PUR", "MASK_general_JPT", "MASK_snp5_JPT", "MASK_general_GIH", "MASK_snp5_GIH", "MASK_general_CH_B", "MASK_snp5_CH_B", "MASK_general_STU", "MASK_snp5_STU", "MASK_general_ITU", "MASK_snp5_ITU", "MASK_general_LWK", "MASK_snp5_LWK", "MASK_general_KHV", "MASK_snp5_KHV", "MASK_general_FIN", "MASK_snp5_FIN", "MASK_general_ESN", "MASK_snp5_ESN", "MASK_general_CEU", "MASK_snp5_CEU", "MASK_general_PJL", "MASK_snp5_PJL", "MASK_general_AC_B", "MASK_snp5_AC_B", "MASK_general_CLM", "MASK_snp5_CLM", "MASK_general_CDX", "MASK_snp5_CDX", "MASK_general_GBR", "MASK_snp5_GBR", "MASK_general_BE_B", "MASK_snp5_BE_B", "MASK_general_PEL", "MASK_snp5_PEL", "MASK_general_MSL", "MASK_snp5_MSL", "MASK_general_MXL", "MASK_snp5_MXL", "MASK_general_ASW", "MASK_snp5_ASW" ], "rows": 865918, "table": true, "tojson": true }, { "name": "hm450.manifest.hg19", "title": "SNP annotation for 450K array.", "object": "hm450.manifest.hg19", "file": "hm450.manifest.hg19.rda", "class": [ "data.frame" ], "fields": [ "CpG_chrm", "CpG_beg", "CpG_end", "probe_strand", "probeID", "address_A", "address_B", "channel", "designType", "nextBase", "nextBaseRef", "probeType", "orientation", "probeCpGcnt", "context35", "probeBeg", "probeEnd", "ProbeSeq_A", "ProbeSeq_B", "gene", "gene_HGNC", "chrm_A", "beg_A", "flag_A", "mapQ_A", "cigar_A", "NM_A", "chrm_B", "beg_B", "flag_B", "mapQ_B", "cigar_B", "NM_B", "wDecoy_chrm_A", "wDecoy_beg_A", "wDecoy_flag_A", "wDecoy_mapQ_A", "wDecoy_cigar_A", "wDecoy_NM_A", "wDecoy_chrm_B", "wDecoy_beg_B", "wDecoy_flag_B", "wDecoy_mapQ_B", "wDecoy_cigar_B", "wDecoy_NM_B", "posMatch", "MASK_mapping", "MASK_typeINextBaseSwitch", "MASK_rmsk15", "MASK_sub40_copy", "MASK_sub35_copy", "MASK_sub30_copy", "MASK_sub25_copy", "MASK_snp5_common", "MASK_snp5_GMAF1p", "MASK_extBase", "MASK_general" ], "rows": 485577, "table": true, "tojson": true }, { "name": "hm450.manifest.pop.hg19", "title": "SNP annotation for 450K array for different population. Data is based on hg19.", "object": "hm450.manifest.pop.hg19", "file": "hm450.manifest.pop.hg19.rda", "class": [ "data.frame" ], "fields": [ "CpG_chrm", "CpG_beg", "CpG_end", "probeID", "MASK_general_AFR", "MASK_snp5_AFR", "MASK_general_EAS", "MASK_snp5_EAS", "MASK_general_EUR", "MASK_snp5_EUR", "MASK_general_SAS", "MASK_snp5_SAS", "MASK_general_AMR", "MASK_snp5_AMR", "MASK_general_GWD", "MASK_snp5_GWD", "MASK_general_YRI", "MASK_snp5_YRI", "MASK_general_TSI", "MASK_snp5_TSI", "MASK_general_IBS", "MASK_snp5_IBS", "MASK_general_CHS", "MASK_snp5_CHS", "MASK_general_PUR", "MASK_snp5_PUR", "MASK_general_JPT", "MASK_snp5_JPT", "MASK_general_GIH", "MASK_snp5_GIH", "MASK_general_CH_B", "MASK_snp5_CH_B", "MASK_general_STU", "MASK_snp5_STU", "MASK_general_ITU", "MASK_snp5_ITU", "MASK_general_LWK", "MASK_snp5_LWK", "MASK_general_KHV", "MASK_snp5_KHV", "MASK_general_FIN", "MASK_snp5_FIN", "MASK_general_ESN", "MASK_snp5_ESN", "MASK_general_CEU", "MASK_snp5_CEU", "MASK_general_PJL", "MASK_snp5_PJL", "MASK_general_AC_B", "MASK_snp5_AC_B", "MASK_general_CLM", "MASK_snp5_CLM", "MASK_general_CDX", "MASK_snp5_CDX", "MASK_general_GBR", "MASK_snp5_GBR", "MASK_general_BE_B", "MASK_snp5_BE_B", "MASK_general_PEL", "MASK_snp5_PEL", "MASK_general_MSL", "MASK_snp5_MSL", "MASK_general_MXL", "MASK_snp5_MXL", "MASK_general_ASW", "MASK_snp5_ASW" ], "rows": 485577, "table": true, "tojson": true }, { "name": "illumina450Gr", "title": "GRange Struct of illumina 450K array.", "object": "illumina450Gr", "file": "illumina450Gr.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "MatchGeneName", "title": "MatchGeneName", "object": "MatchGeneName", "file": "MatchGeneName.rda", "class": [ "data.frame" ], "fields": [ "V2", "V3" ], "rows": 33483, "table": true, "tojson": true }, { "name": "multi.hit", "title": "multi.hit information.", "object": "multi.hit", "file": "multi.hit.rda", "class": [ "data.frame" ], "fields": [ "TargetID", "INFINIUM_DESIGN_TYPE", "GENOME_BUILD", "CHR", "MAPINFO", "CHROMOSOME_36", "COORDINATE_36", "STRAND", "UCSC_REFGENE_NAME", "UCSC_REFGENE_ACCESSION", "UCSC_REFGENE_GROUP", "UCSC_CPG_ISLANDS_NAME", "RELATION_TO_UCSC_CPG_ISLAND", "SNP", "SNP_DISTANCE", "snp.hit", "bwa.multi.hit", "analyzed", "DNase", "h3k4me3", "h3k36me3", "h3k27ac", "h3k4me1", "bivalent", "h3k27me3", "h3k9me3", "dmc.constitutive", "dmc.relapse", "dmc.T", "dmc.MLL", "dmc.dic920", "dmc.HeH", "dmc.t119", "dmc.t1221", "dmc.t922", "dmc.iamp", "dmc.undefined", "dmc.nonrecurrent" ], "rows": 9341, "table": true, "tojson": true }, { "name": "PathwayList", "title": "PathwayList, used in champ.GSEA()", "object": "PathwayList", "file": "PathwayList.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "probe.features", "title": "probe.features", "object": "probe.features", "file": "probe.features.epic.rda", "class": [ "data.frame" ], "fields": [ "CHR", "MAPINFO", "Strand", "Type", "gene", "feature", "cgi", "feat.cgi", "UCSC_CpG_Islands_Name", "DHS", "Enhancer", "Phantom", "Probe_SNPs", "Probe_SNPs_10" ], "rows": 485577, "table": true, "tojson": true }, { "name": "probeInfoALL.lv", "title": "Probe Info Data for use with the BMIQ normalization.", "object": "probeInfoALL.lv", "file": "probeInfoALL.lv.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "snp.hit", "title": "CpG site related to SNP sites information.", "object": "snp.hit", "file": "snp.hit.rda", "class": [ "data.frame" ], "fields": [ "TargetID", "INFINIUM_DESIGN_TYPE", "GENOME_BUILD", "CHR", "MAPINFO", "CHROMOSOME_36", "COORDINATE_36", "STRAND", "UCSC_REFGENE_NAME", "UCSC_REFGENE_ACCESSION", "UCSC_REFGENE_GROUP", "UCSC_CPG_ISLANDS_NAME", "RELATION_TO_UCSC_CPG_ISLAND", "SNP", "SNP_DISTANCE", "snp.hit", "bwa.multi.hit", "analyzed", "DNase", "h3k4me3", "h3k36me3", "h3k27ac", "h3k4me1", "bivalent", "h3k27me3", "h3k9me3", "dmc.constitutive", "dmc.relapse", "dmc.T", "dmc.MLL", "dmc.dic920", "dmc.HeH", "dmc.t119", "dmc.t1221", "dmc.t922", "dmc.iamp", "dmc.undefined", "dmc.nonrecurrent" ], "rows": 29481, "table": true, "tojson": true } ], "_help": [ { "page": "ChAMPdata-package", "title": "Data Packages to use with the ChAMP Chip Analysis Methylation Pipeline", "topics": [ "ChAMPdata-package", "ChAMPdata" ] }, { "page": "Anno450K", "title": "Anno450K", "topics": [ "Anno450K" ] }, { "page": "AnnoEPIC", "title": "AnnoEPIC", "topics": [ "AnnoEPIC" ] }, { "page": "bloodCtl", "title": "Blood Control data", "topics": [ "bloodCtl" ] }, { "page": "CellTypeMeans27K", "title": "Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.", "topics": [ "CellTypeMeans27K" ] }, { "page": "CellTypeMeans450K", "title": "Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.", "topics": [ "CellTypeMeans450K" ] }, { "page": "ControlProbes450K", "title": "ControlProbes450K", "topics": [ "ControlProbes450K" ] }, { "page": "ControlProbesEPIC", "title": "ControlProbesEPIC", "topics": [ "ControlProbesEPIC" ] }, { "page": "EPIC.manifest.hg19", "title": "SNP annotation for EPIC array.", "topics": [ "EPIC.manifest.hg19" ] }, { "page": "EPIC.manifest.pop.hg19", "title": "SNP annotation for EPIC array for different population.", "topics": [ "EPIC.manifest.pop.hg19" ] }, { "page": "EPICSimData", "title": "Simulation EPIC beadarray Dataset.", "topics": [ "EPICSimData" ] }, { "page": "hm450.manifest.hg19", "title": "SNP annotation for 450K array.", "topics": [ "hm450.manifest.hg19" ] }, { "page": "hm450.manifest.pop.hg19", "title": "SNP annotation for 450K array for different population. Data is based on hg19.", "topics": [ "hm450.manifest.pop.hg19" ] }, { "page": "hprdAsigH", "title": "hprdAsigH PPI network dataset for champ.FEM function.", "topics": [ "hprdAsigH" ] }, { "page": "illumina450Gr", "title": "GRange Struct of illumina 450K array.", "topics": [ "illumina450Gr" ] }, { "page": "illuminaEPICGr", "title": "GRange S4 Object of illumina EPIC array.", "topics": [ "illuminaEPICGr" ] }, { "page": "MatchGeneName", "title": "MatchGeneName", "topics": [ "MatchGeneName" ] }, { "page": "multi.hit", "title": "multi.hit information.", "topics": [ "multi.hit" ] }, { "page": "PathwayList", "title": "PathwayList, used in champ.GSEA()", "topics": [ "PathwayList" ] }, { "page": "probe.features", "title": "probe.features", "topics": [ "probe.features" ] }, { "page": "probe.features.epic", "title": "probe.features.epic", "topics": [ "probe.features.epic" ] }, { "page": "probeInfoALL.epic.lv", "title": "Probe Info Data for use with the BMIQ normalization.", "topics": [ "probeInfoALL.epic.lv" ] }, { "page": "probeInfoALL.lv", "title": "Probe Info Data for use with the BMIQ normalization.", "topics": [ "probeInfoALL.lv" ] }, { "page": "snp.hit", "title": "CpG site related to SNP sites information.", "topics": [ "snp.hit" ] }, { "page": "testDataSet", "title": "Test dataset.", "topics": [ "testDataSet" ] } ], "_rundeps": [ "BiocGenerics", "generics", "GenomicRanges", "IRanges", "S4Vectors", "Seqinfo" ], "_score": 4.147367107793786, "_indexed": true, "_nocasepkg": "champdata", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.45.1", "date": "2026-10-10T11:07:46.000Z", "distro": "resolute", "commit": "5eb766f3651df6e06e498c80790a793393e6c25c", "fileid": "https://r2.ropensci.org/8c03f6421d7103c4a3747fb8a01c95a09a55e0cc5090f9dea9c31b7fcf115ed2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045093705" }, { "r": "4.6.1", "os": "linux", "version": "2.45.1", "date": "2026-10-10T11:07:53.000Z", "distro": "resolute", "commit": "5eb766f3651df6e06e498c80790a793393e6c25c", "fileid": "https://r2.ropensci.org/aebb6bc41f7f8706affb30d63038d52322ab90422da8c4bd7f1abef918a8761d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38045093705" } ] }