mCSEAdata package contains the necessary files to run the core analysis in mCSEA package. It also contains example data used by mCSEA to show it’s functionality.
mCSEAdata 1.29.1
library(mCSEAdata)
data(mcseadata)
data(bandTable)Firstly, betaTest, phenoTest and exprTest are the objects necessary to run the examples in mCSEA package. betaTest is a matrix with the beta-values of 9241 EPIC probes for 20 samples. exprTest is a subset of 100 genes’ expression from bone marrows of 10 healthy and 10 leukemia patients. phenoTest is a dataframe with the explanatory variable and covariates associated to the samples.
class(betaTest)## [1] "matrix" "array"dim(betaTest)## [1] 9241 20head(betaTest, 3)## 1 2 3 4 5 6
## cg18478105 0.6845279 0.6917252 0.8622046 0.6966168 0.1204777 0.7670960
## cg10605442 0.1370685 0.8450987 0.5480076 0.8671236 0.8300113 0.1667405
## cg27657131 0.1333706 0.6745949 0.8702664 0.9338893 0.8788454 0.1853554
## 7 8 9 10 11 12
## cg18478105 0.93804510 0.88166619 0.90385504 0.9287976 0.04052779 0.10765614
## cg10605442 0.08727434 0.10568040 0.11896201 0.1764874 0.73534148 0.05741730
## cg27657131 0.10463463 0.05660229 0.06469281 0.2235293 0.92030432 0.04618165
## 13 14 15 16 17 18
## cg18478105 0.1459481 0.8334884 0.1209040 0.07747453 0.7001099 0.7528026
## cg10605442 0.8213965 0.8208602 0.1671381 0.10157830 0.8874912 0.1723724
## cg27657131 0.1374107 0.8432675 0.9642680 0.14536637 0.9372422 0.9315385
## 19 20
## cg18478105 0.86687272 0.85999403
## cg10605442 0.88836050 0.06521765
## cg27657131 0.06357636 0.50609450class(phenoTest)## [1] "data.frame"dim(phenoTest)## [1] 20 2head(phenoTest, 3)## expla cov1
## 1 Case 1
## 2 Case 2
## 3 Case 1class(exprTest)## [1] "matrix" "array"dim(exprTest)## [1] 100 20head(exprTest, 3)## 1 2 3 4 5 6 7
## ENSG00000179023 4.145748 4.388779 4.265583 4.374576 4.463465 4.078678 4.335878
## ENSG00000179029 4.485414 5.044662 5.411474 5.590093 5.365381 4.951236 6.626413
## ENSG00000179041 6.618769 6.443408 7.642324 7.989362 7.133374 7.224613 5.853054
## 8 9 10 11 12 13 14
## ENSG00000179023 4.121601 4.163271 4.219654 4.340421 3.917131 4.284802 4.161627
## ENSG00000179029 5.070305 5.582466 5.688895 5.675448 5.053258 5.708689 5.170988
## ENSG00000179041 8.198245 6.847891 6.598557 6.546835 7.211352 7.190893 6.825418
## 15 16 17 18 19 20
## ENSG00000179023 4.308718 4.074333 4.171878 4.083548 4.549825 4.199466
## ENSG00000179029 5.480265 5.118550 5.657001 5.257061 5.677323 5.171198
## ENSG00000179041 7.342032 7.309422 6.831020 7.728485 7.214401 6.781880On the other hand, there are 9 association objects. Each one is a list of features with their associated 450k, EPIC and EPICv2 CpG probes. The features included are promoters (assocPromoters450k, assocPromotersEPIC and assocPromotersEPICv2), gene bodies (assocGenes450k, assocGenesEPIC and assocGenesEPICv2) and CpG islands (assocCGI450k, assocCGIEPIC and assocCGIEPICv2). These objects are internally used by mCSEA.test function in mCSEA package.
class(assocPromoters450k)## [1] "list"length(assocPromoters450k)## [1] 20960head(assocPromoters450k, 3)## $FAM197Y2
## [1] "cg00050873" "cg03052502" "cg03443143" "cg17834650" "cg02802508"
## [6] "cg03535417" "cg08635406" "cg17769199"
##
## $TTTY14
## [1] "cg00212031" "cg15345074" "cg06628792" "cg11684211" "cg11816202"
##
## $TMSB4Y
## [1] "cg00214611" "cg02004872" "cg02730008" "cg26198148"class(assocGenes450k)## [1] "list"length(assocGenes450k)## [1] 19071head(assocGenes450k, 3)## $TSPY4
## [1] "cg00050873" "cg03443143" "cg04016144" "cg05544622" "cg09350919"
## [6] "cg15810474" "cg15935877" "cg17834650" "cg17837162" "cg25705492"
## [11] "cg00543493" "cg00903245" "cg01523029" "cg02606988" "cg02802508"
## [16] "cg03535417" "cg04958669" "cg08258654" "cg08635406" "cg10239257"
## [21] "cg13861458" "cg14005657" "cg25538674" "cg26475999"
##
## $TTTY14
## [1] "cg03244189" "cg05230942" "cg10811597" "cg13765957" "cg13845521"
## [6] "cg15281205" "cg26251715"
##
## $NLGN4Y
## [1] "cg03706273" "cg25518695" "cg01073572" "cg01498999" "cg02340092"
## [6] "cg03278611" "cg04419680" "cg05939513" "cg07795413" "cg08816194"
## [11] "cg09300505" "cg09748856" "cg09804407" "cg10990737" "cg18113731"
## [16] "cg19244032" "cg27214488" "cg27265812" "cg27443332"class(assocCGI450k)## [1] "list"length(assocCGI450k)## [1] 27176head(assocCGI450k, 3)## $`chrY:9363680-9363943`
## [1] "cg00050873" "cg03443143"
##
## $`chrY:21238448-21240005`
## [1] "cg00212031" "cg03244189" "cg15345074" "cg06628792" "cg10811597"
## [6] "cg11684211" "cg11816202" "cg13845521" "cg26251715"
##
## $`chrY:8147877-8148210`
## [1] "cg00213748" "cg02272584" "cg06237805" "cg08160949" "cg08702825"
## [6] "cg08739478"class(assocPromotersEPIC)## [1] "list"length(assocPromotersEPIC)## [1] 26208head(assocPromotersEPIC, 3)## $YTHDF1
## [1] "cg18478105" "cg10605442" "cg27657131" "cg08514185" "cg13587582"
## [6] "cg25802399" "cg22485414" "cg03501095" "cg24092253" "cg12589387"
##
## $EIF2S3
## [1] "cg09835024" "cg06127902" "cg12275687" "cg00914804" "cg27345735"
## [6] "cg12590845" "cg25034591" "cg16712639" "cg07622257"
##
## $PKN3
## [1] "cg14361672" "cg06550760" "cg14204415" "cg11056832" "cg14036226"
## [6] "cg22365023" "cg20593100"class(assocGenesEPIC)## [1] "list"length(assocGenesEPIC)## [1] 23772head(assocGenesEPIC, 3)## $CCDC57
## [1] "cg01763666" "cg26701563" "cg16920238" "cg17286790" "cg11989942"
## [6] "cg03388043" "cg05483915" "cg05915375" "cg04098763" "cg14090409"
## [11] "cg21295367" "cg20780302" "cg01465684" "cg18209359" "cg16578864"
## [16] "cg15754222" "cg21880101" "cg05522083" "cg12952529" "cg14673194"
## [21] "cg10477817" "cg17751591" "cg11719141" "cg26928858" "cg21698718"
## [26] "cg07310278" "cg13339291" "cg13367490" "cg12336460" "cg02208313"
## [31] "cg26507988" "cg15857073" "cg22476252" "cg11935831" "cg08864681"
## [36] "cg22167267" "cg14832684" "cg09804706" "cg24973483" "cg12486944"
## [41] "cg00412514" "cg13796123" "cg13000015" "cg04824810" "cg25639749"
## [46] "cg03789597" "cg14136083" "cg13855717" "cg25612997" "cg20880890"
## [51] "cg04955630" "cg19976037" "cg16849440" "cg25735697" "cg22312907"
## [56] "cg12223090" "cg02967812" "cg04210266" "cg26837952" "cg06493125"
## [61] "cg08047030" "cg20798760" "cg00755572" "cg25388952" "cg13198984"
## [66] "cg01216201" "cg19567758" "cg22882093" "cg24480260" "cg23985595"
## [71] "cg06073302" "cg16477682" "cg25532751" "cg20299209" "cg11716677"
## [76] "cg02094669" "cg11859384" "cg10505658" "cg21577598" "cg24963024"
## [81] "cg17251650" "cg24378699" "cg02262688" "cg06132853" "cg22491947"
## [86] "cg02200666" "cg07959490" "cg09163921" "cg18996153" "cg20197093"
## [91] "cg18151291" "cg22142205" "cg16124601" "cg26105045" "cg23522485"
## [96] "cg16279483" "cg26093898" "cg21565972"
##
## $INF2
## [1] "cg12950382" "cg18425377" "cg09184385" "cg10533694" "cg20980960"
## [6] "cg07039149" "cg18519050" "cg23206460" "cg05210373" "cg03576530"
## [11] "cg25592858" "cg18996808" "cg10345522" "cg08043200" "cg17331554"
## [16] "cg03719908" "cg18465331" "cg23956771" "cg21827986" "cg14377342"
## [21] "cg24404909" "cg00816970" "cg23601271" "cg04966159" "cg18924331"
## [26] "cg22090592" "cg04278105" "cg12031670" "cg26212352" "cg02878289"
## [31] "cg05018513" "cg06971503" "cg11290775" "cg23343291" "cg18447460"
##
## $PIP5K1C
## [1] "cg26724186" "cg05809578" "cg05233128" "cg17845617" "cg25247177"
## [6] "cg02322048" "cg19423978" "cg16583193" "cg20969388" "cg08145067"
## [11] "cg15564488" "cg07577499" "cg03228408" "cg24732692" "cg09288755"
## [16] "cg02952625" "cg13995193" "cg11243391" "cg00793543" "cg27490930"
## [21] "cg19841005" "cg10591771" "cg10490670" "cg06358131" "cg16019751"
## [26] "cg22848927" "cg21865657" "cg19736470" "cg11955890" "cg07479621"
## [31] "cg17791316" "cg05312862" "cg07907254" "cg15483758" "cg02818004"
## [36] "cg06724384" "cg07059636" "cg17097293" "cg22623033" "cg01168835"
## [41] "cg13588224" "cg15389497" "cg23249839" "cg23480820" "cg13561409"
## [46] "cg17820448" "cg08301518" "cg17698261" "cg22677650" "cg03540494"
## [51] "cg15200445" "cg16248034" "cg14093663" "cg16564917" "cg07963254"
## [56] "cg02859655" "cg02106453" "cg00376288" "cg17290669" "cg20750693"
## [61] "cg12557799" "cg01070272" "cg06497674" "cg04385058" "cg00438838"
## [66] "cg10996109" "cg18249653" "cg06587767" "cg13670756" "cg04801430"
## [71] "cg12298375" "cg23654206" "cg15080709" "cg15540507" "cg08267629"
## [76] "cg11976007" "cg11452653" "cg09547756" "cg04742624"class(assocCGIEPIC)## [1] "list"length(assocCGIEPIC)## [1] 27187head(assocCGIEPIC, 3)## $`chr20:61846843-61848103`
## [1] "cg18478105" "cg10605442" "cg27657131" "cg08514185" "cg17364922"
## [6] "cg13587582" "cg25802399" "cg22485414" "cg15407723" "cg03501095"
## [11] "cg02177162" "cg10201192" "cg13388572" "cg00624976" "cg24092253"
## [16] "cg12589387"
##
## $`chrX:24072558-24073135`
## [1] "cg09835024" "cg06127902" "cg12275687" "cg00914804" "cg27345735"
## [6] "cg12590845" "cg25034591" "cg16712639" "cg07622257"
##
## $`chr9:131464843-131465830`
## [1] "cg14361672" "cg06550760" "cg14204415" "cg07950002" "cg11056832"
## [6] "cg14036226" "cg22365023" "cg20593100" "cg13548833"class(assocPromotersEPICv2)## [1] "list"length(assocPromotersEPICv2)## [1] 26153head(assocPromotersEPICv2, 3)## $ZNF781
## [1] "cg25324105_BC11" "cg22521696_TC11" "cg25875213_TC11" "cg17445666_TC11"
## [5] "cg04784475_TC11" "cg03611452_TC11" "cg14587524_BC11" "cg22685966_BC21"
## [9] "cg17182700_TC21" "cg10701051_BC21"
##
## $ETNK2
## [1] "cg25623721_TC11" "cg20136584_TC11" "cg04913057_TC11" "cg08114257_TC11"
## [5] "cg01486694_BC11" "cg01566404_BC21" "cg25512657_BC21" "cg00103329_TC21"
## [9] "cg21535580_TC21" "cg11687966_BC21" "cg12549161_BC21"
##
## $`PPM1F-AS1`
## [1] "cg25898577_BC11" "cg27653384_TC11" "cg26102199_BC21" "cg01612629_TC21"
## [5] "cg01052666_TC21" "cg03086022_BC21" "cg17159137_BC21" "cg25225310_TC21"
## [9] "cg15736557_BC21" "cg04524370_BC21" "cg14641478_TC21" "cg25923015_TC21"
## [13] "cg05160769_BC21" "cg25405702_BC21" "cg17570088_TC21" "cg26102189_TC21"
## [17] "cg26102184_TC21"class(assocGenesEPICv2)## [1] "list"length(assocGenesEPICv2)## [1] 18614head(assocGenesEPICv2, 3)## $ACTN4
## [1] "cg25383568_TC11" "cg03575974_BC11" "cg03575974_BC12" "cg03575974_BC13"
## [5] "cg24500219_BC11" "cg01030321_TC21" "cg16814576_BC21" "cg23197406_TC21"
## [9] "cg24499830_BC21" "cg07001793_BC21" "cg06540331_BC21" "cg19484260_TC21"
## [13] "cg24500564_TC21" "cg24500541_BC21" "cg24500217_BC21"
##
## $FAM171A2
## [1] "cg23766254_TC11" "cg22078805_BC11" "cg19935040_BC11" "cg17624802_BC11"
## [5] "cg15909132_TC11" "cg09014329_TC21" "cg05622422_BC21"
##
## $CLPTM1L
## [1] "cg26224791_TC11" "cg17304712_TC11" "cg07576613_TC11" "cg14631690_TC11"
## [5] "cg08433725_TC21" "cg25692669_BC21" "cg20700235_TC21" "cg07385490_TC21"
## [9] "cg07162264_BC21" "cg21891499_BC21" "cg08547617_TC21"class(assocCGIEPICv2)## [1] "list"length(assocCGIEPICv2)## [1] 25805head(assocCGIEPICv2, 3)## $`chr19:37691892-37692426`
## [1] "cg25324105_BC11" "cg22521696_TC11" "cg09449030_TC11" "cg25875213_TC11"
## [5] "cg17445666_TC11" "cg04784475_TC11" "cg03611452_TC11" "cg14587524_BC11"
##
## $`chr19:38726890-38727217`
## [1] "cg25383568_TC11" "cg04517274_TC21"
##
## $`chr19:1591428-1591629`
## [1] "cg25455143_BC11" "cg24140597_BC11" "cg08660999_TC11" "cg12286540_TC11"
## [5] "cg08704080_TC11" "cg22069171_BC11" "cg26982998_BC21" "cg09174855_TC21"
## [9] "cg21739009_BC21"There are also 3 GRanges objects with the locations of 450K, EPIC and EPICv2 probes, used by mCSEAPlot() and mCSEAIntegrate() functions:
class(annot450K)## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"head(annot450K, 3)## GRanges object with 3 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## cg00050873 chrY 9363356 *
## cg00212031 chrY 21239348 *
## cg00213748 chrY 8148233 *
## -------
## seqinfo: 24 sequences from hg19 genome; no seqlengthsclass(annotEPIC)## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"head(annotEPIC, 3)## GRanges object with 3 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## cg18478105 chr20 61847650 *
## cg09835024 chrX 24072640 *
## cg14361672 chr9 131463936 *
## -------
## seqinfo: 24 sequences from hg19 genome; no seqlengthsclass(annotEPICv2)## [1] "GRanges"
## attr(,"package")
## [1] "GenomicRanges"head(annotEPICv2, 3)## GRanges object with 3 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## cg25324105_BC11 chr19 37692358 +
## cg25383568_TC11 chr19 38727081 -
## cg25455143_BC11 chr19 1591515 -
## -------
## seqinfo: 24 sequences from an unspecified genome; no seqlengthsFinally, bandTable object contains two objects with the information of chromosomes band information and centromer location, one for each genome building: hg19 and hg38 It is used by mCSEAPlot() function to plot the chromosome track.
head(bandTablehg19)## chrom chromStart chromEnd name gieStain
## 1 chr1 0 2300000 p36.33 gneg
## 2 chr1 2300000 5400000 p36.32 gpos25
## 3 chr1 5400000 7200000 p36.31 gneg
## 4 chr1 7200000 9200000 p36.23 gpos25
## 5 chr1 9200000 12700000 p36.22 gneg
## 6 chr1 12700000 16200000 p36.21 gpos50head(bandTablehg38)## chrom chromStart chromEnd name gieStain
## 1 chr1 0 2300000 p36.33 gneg
## 2 chr1 2300000 5300000 p36.32 gpos25
## 3 chr1 5300000 7100000 p36.31 gneg
## 4 chr1 7100000 9100000 p36.23 gpos25
## 5 chr1 9100000 12500000 p36.22 gneg
## 6 chr1 12500000 15900000 p36.21 gpos50| Region type | mCSEAdata association objects | Column from association DataFrame used | Column values | Feature name column |
|---|---|---|---|---|
| Promoters | assocPromoters450k, assocPromotersEPIC and assocPromotersEPICv2 | UCSC_RefGene_Group | TSS1500, TSS200, 5’UTR, 1stExon or exon_1 | UCSC_RefGene_Name |
| Gene bodies | assocGenes450k, assocGenesEPIC and assocGenesEPICv2 | UCSC_RefGene_Group | Body | UCSC_RefGene_Name |
| CpG Islands | assocCGI450k, assocCGIEPIC and assocCGIEPICv2 | Relation_to_Island | Island, N_Shore, S_Shore, N_Shelf or S_Shelf | Islands_Name |
For instance, cg00212031 probe from 450k platform has the following annotation data in the association DataFrame:
| UCSC_RefGene_Group | UCSC_RefGene_Name | Relation_to_Island | Islands_Name |
|---|---|---|---|
| TSS200 | TTTY14 | Island | chrY:21238448-21240005 |
So this probe is associated to TTTY14 promoter in assocPromoters450k object and to chrY:21238448-21240005 CpG Island in assocCGI450k object.
Annotation objects (annot450K, annotEPIC and annotEPICv2): They were both constructed with minfi package. A RGChannelSet object was obtained for each platform and getLocations() function was applied to such objects.
bandTablehg19 and bandTablehg38: It was constructed with Gviz package, concretely with IdeogramTrack() function.
## R version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] mCSEAdata_1.29.1 BiocStyle_2.37.1
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.5 knitr_1.50 rlang_1.1.6
## [4] xfun_0.53 generics_0.1.4 jsonlite_2.0.0
## [7] S4Vectors_0.47.4 htmltools_0.5.8.1 sass_0.4.10
## [10] stats4_4.5.1 rmarkdown_2.30 Seqinfo_0.99.3
## [13] evaluate_1.0.5 jquerylib_0.1.4 fastmap_1.2.0
## [16] yaml_2.3.10 IRanges_2.43.5 lifecycle_1.0.4
## [19] bookdown_0.45 BiocManager_1.30.26 compiler_4.5.1
## [22] XVector_0.49.1 digest_0.6.37 R6_2.6.1
## [25] GenomicRanges_1.61.6 bslib_0.9.0 tools_4.5.1
## [28] BiocGenerics_0.55.4 cachem_1.1.0