Get DNA methylation EPIC data for the example.
## $GSE86831_series_matrix.txt.gz
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 864935 features, 15 samples
## element names: exprs
## protocolData: none
## phenoData
## sampleNames: GSM2309170 GSM2309171 ... GSM2309184 (15 total)
## varLabels: title geo_accession ... tissue:ch1 (33 total)
## varMetadata: labelDescription
## featureData
## featureNames: cg00000029 cg00000103 ... cg27666123 (864935 total)
## fvarLabels: ID SPOT_ID ... SourceSeq (14 total)
## fvarMetadata: Column Description labelDescription
## experimentData: use 'experimentData(object)'
## pubMedIds: 27717381
## Annotation: GPL21145epic.matrix <- gse86831$GSE86831_series_matrix.txt.gz %>% exprs
colnames(epic.matrix) <- paste0("C3L.000",1:15)
epic.matrix %>% dim()## [1] 864935 15## C3L.0001 C3L.0002 C3L.0003 C3L.0004 C3L.0005 C3L.0006
## cg00000029 0.8283680 0.8354139 0.05658668 0.04282275 0.35627030 0.20198010
## cg00000103 0.2164977 0.2394069 0.39861730 0.35705640 0.66447370 0.45222250
## cg00000109 0.8251206 0.7513673 0.77963550 0.83643360 0.74479860 0.81600280
## cg00000155 0.9184039 0.9028827 0.90118500 0.91898540 0.90891310 0.92960120
## cg00000158 0.9168520 0.9113715 0.93191020 0.91307780 0.92690950 0.92782270
## cg00000165 0.8359243 0.8572026 0.07873143 0.09703349 0.07308517 0.07546386
## C3L.0007 C3L.0008 C3L.0009 C3L.00010 C3L.00011 C3L.00012
## cg00000029 0.32439100 0.20218200 0.41619230 0.54138310 0.5338212 0.5665801
## cg00000103 0.40891410 0.57256860 0.62188910 0.78878380 0.8677205 0.8803490
## cg00000109 0.86966160 0.85955420 0.68624070 0.77484770 0.8659036 0.8849434
## cg00000155 0.87370890 0.91478070 0.91392830 0.89565840 0.9080459 0.9212264
## cg00000158 0.93755640 0.93855110 0.88565760 0.93266590 0.8981978 0.9033220
## cg00000165 0.06433051 0.06738134 0.04520237 0.06496383 0.1230667 0.1254290
## C3L.00013 C3L.00014 C3L.00015
## cg00000029 0.60287830 0.5380207 0.5494488
## cg00000103 0.90468330 0.8709923 0.9216082
## cg00000109 0.86523140 0.9000149 0.8982691
## cg00000155 0.89568590 0.9346259 0.9231887
## cg00000158 0.91580930 0.9110322 0.9097360
## cg00000165 0.08090399 0.1103282 0.1544130library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-ACC",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - FPKM-UQ")
GDCdownload(query)
rna <- GDCprepare(query,summarizedExperiment = FALSE)
rna <- rna %>% as.data.frame()
rownames(rna) <- gsub("\\.[0-9]*","",rna$X1)
rna$X1 <- NULL
rna <- rna[,1:15]## [1] 60483 15# Create matrix with metadata
colData <- data.frame(row.names = colnames(rna),
"primary" = colnames(rna),
"Group" = c(rep("A",7),
rep("B", 8)))
colData## Returning distal probes: 342877mae <- createMAE(exp = rna,
met = epic.matrix,
TCGA = FALSE,
filter.probes = distal.enhancer,
colData = colData,
linearize.exp = TRUE,
genome = "hg38")## =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-## Creating a SummarizedExperiment from gene expression input## =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-## Creating a SummarizedExperiment from DNA methylation input## Removing samples not found in both DNA methylation and gene expression (we are considering the names of the gene expression and DNA methylation columns to be the same)## MAE saved as: mae_hg38_450K.rda## A MultiAssayExperiment object of 2 listed
## experiments with user-defined names and respective classes.
## Containing an ExperimentList class object of length 2:
## [1] DNA methylation: RangedSummarizedExperiment with 148376 rows and 15 columns
## [2] Gene expression: RangedSummarizedExperiment with 56602 rows and 15 columns
## Features:
## experiments() - obtain the ExperimentList instance
## colData() - the primary/phenotype DFrame
## sampleMap() - the sample availability DFrame
## `$`, `[`, `[[` - extract colData columns, subset, or experiment
## *Format() - convert into a long or wide DFrame
## assays() - convert ExperimentList to a SimpleList of matrices## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 19.10
## system x86_64, linux-gnu
## ui X11
## language en_US
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-02-06
##
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