1 Package contents

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   20

head(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 0.50609450

class(phenoTest)

## [1] "data.frame"

dim(phenoTest)

## [1] 20  2

head(phenoTest, 3)

##   expla cov1
## 1  Case    1
## 2  Case    2
## 3  Case    1

class(exprTest)

## [1] "matrix" "array"

dim(exprTest)

## [1] 100  20

head(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 6.781880

On the other hand, there are 6 association objects. Each one is a list of features with their associated 450k or EPIC CpG probes. The features included are promoters (assocPromoters450k and assocPromotersEPIC), gene bodies (assocGenes450k and assocGenesEPIC) and CpG islands (assocCGI450k and assocCGIEPIC). These objects are internally used by mCSEA.test function in mCSEA package.

class(assocPromoters450k)

## [1] "list"

length(assocPromoters450k)

## [1] 20960

head(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] 19071

head(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] 27176

head(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] 26208

head(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] 23772

head(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] 27187

head(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"

There are also 2 GRanges objects with the locations of 450K and EPIC 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 seqlengths

class(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 seqlengths

Finally, bandTable object contains chromosomes band information and centromer location. It is used by mCSEAPlot() function to plot the chromosome track.

head(bandTable)

##   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   gpos50

2 Sources

Example objects:
- betaTest contains simulated beta-values for EPIC platform probes.
- exprTest contains expression data from Leukemia and healthy patients extracted from leukemiaEset package.
- phenoTest contains arbitrary phenotypes for each sample.
Association objects: They were all constructed from IlluminaHumanMethylation450kanno.ilmn12.hg19 and IlluminaHumanMethylationEPICanno.ilm10b2.hg19 packages annotation data. For that purpose, a RGChannelSet object was obtained with minfi package and getAnnotation() function was applied to such object in order to get the annotation DataFrame. That was done for both 450k and EPIC platforms. The annotation DataFrame contains several information about each CpG probe, and we used that information to associate each probe to one or more promoter, gene body or CpG Island following this scheme:

Region type	mCSEAdata association objects	Column from association DataFrame used	Column values	Feature name column
Promoters	assocPromoters450k and assocPromotersEPIC	UCSC_RefGene_Group	TSS1500, TSS200, 5’UTR or 1stExon	UCSC_RefGene_Name
Gene bodies	assocGenes450k and assocGenesEPIC	UCSC_RefGene_Group	Body	UCSC_RefGene_Name
CpG Islands	assocCGI450k and assocCGIEPIC	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 and annotEPIC): They were both constructed with minfi package. A RGChannelSet object was obtained for each platform and getLocations() function was applied to such objects.
bandTable: It was constructed with Gviz package, concretely with IdeogramTrack() function.

3 Session info

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0  IRanges_2.40.0      
## [4] S4Vectors_0.44.0     BiocGenerics_0.52.0  mCSEAdata_1.26.1    
## [7] BiocStyle_2.34.0    
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.7              cli_3.6.3               knitr_1.49             
##  [4] rlang_1.1.4             xfun_0.49               UCSC.utils_1.2.0       
##  [7] jsonlite_1.8.9          htmltools_0.5.8.1       sass_0.4.9             
## [10] rmarkdown_2.29          evaluate_1.0.1          jquerylib_0.1.4        
## [13] fastmap_1.2.0           yaml_2.3.10             lifecycle_1.0.4        
## [16] bookdown_0.41           BiocManager_1.30.25     compiler_4.4.2         
## [19] XVector_0.46.0          digest_0.6.37           R6_2.5.1               
## [22] GenomeInfoDbData_1.2.13 bslib_0.8.0             tools_4.4.2            
## [25] zlibbioc_1.52.0         cachem_1.1.0

Data for mCSEA package

28 November 2024

Abstract

Package

Contents

1 Package contents

2 Sources

3 Session info