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CHECK report for MultiAssayExperiment on malbec1

This page was generated on 2018-04-12 13:14:47 -0400 (Thu, 12 Apr 2018).

Package 909/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiAssayExperiment 1.4.9
Marcel Ramos
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MultiAssayExperiment
Branch: RELEASE_3_6
Last Commit: bf2ee26
Last Changed Date: 2018-01-06 21:04:02 -0400 (Sat, 06 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MultiAssayExperiment
Version: 1.4.9
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.4.9.tar.gz
StartedAt: 2018-04-12 01:20:29 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:22:58 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 148.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MultiAssayExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MultiAssayExperiment_1.4.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MultiAssayExperiment.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiAssayExperiment/DESCRIPTION’ ... OK
* this is package ‘MultiAssayExperiment’ version ‘1.4.9’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MultiAssayExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MultiAssayExperiment.Rcheck/00check.log’
for details.

Installation output

MultiAssayExperiment.Rcheck/00install.out

* installing *source* package ‘MultiAssayExperiment’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MultiAssayExperiment)

Tests output

MultiAssayExperiment.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MultiAssayExperiment)
> 
> test_check("MultiAssayExperiment")

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)

MltAsE> ## Run the example ExperimentList
MltAsE> example("ExperimentList")

ExprmL> ## Create an empty ExperimentList instance
ExprmL> ExperimentList()
ExperimentList class object of length 0:  

ExprmL> ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
ExprmL> arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000294241", "ENST00000355076",
ExprmL+         "ENST00000383706","ENST00000234812", "ENST00000383323"),
ExprmL+         c("array1", "array2", "array3", "array4")
ExprmL+     ))

ExprmL> arraypdat <- as(data.frame(
ExprmL+     slope53 = rnorm(4),
ExprmL+     row.names = c("array1", "array2", "array3", "array4")),
ExprmL+     "AnnotatedDataFrame")

ExprmL> ## ExpressionSet constructor
ExprmL> exprdat <- Biobase::ExpressionSet(assayData = arraydat, phenoData = arraypdat)

ExprmL> ## Create a sample methylation dataset
ExprmL> methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
ExprmL+     dimnames = list(
ExprmL+         c("ENST00000355076", "ENST00000383706",
ExprmL+           "ENST00000383323", "ENST00000234812", "ENST00000294241"),
ExprmL+         c("methyl1", "methyl2", "methyl3",
ExprmL+           "methyl4", "methyl5")
ExprmL+     ))

ExprmL> ## Create a sample RNASeqGene dataset
ExprmL> rnadat <- matrix(
ExprmL+     data = sample(c(46851, 5, 19, 13, 2197, 507,
ExprmL+         84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
ExprmL+     ncol = 4,
ExprmL+     dimnames = list(
ExprmL+         c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
ExprmL+         c("samparray1", "samparray2", "samparray3", "samparray4")
ExprmL+     ))

ExprmL> ## Combine to a named list and call the ExperimentList constructor function
ExprmL> ExpList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat)

ExprmL> ## Use the ExperimentList constructor
ExprmL> myExperimentList <- ExperimentList(ExpList)

MltAsE> ## Create sample maps for each experiment
MltAsE> exprmap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("array1", "array2", "array3", "array4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> methylmap <- data.frame(
MltAsE+     primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
MltAsE+     colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> rnamap <- data.frame(
MltAsE+     primary = c("Jack", "Jill", "Bob", "Barbara"),
MltAsE+     colname = c("samparray1", "samparray2", "samparray3",
MltAsE+                                "samparray4"),
MltAsE+     stringsAsFactors = FALSE)

MltAsE> ## Combine as a named list and convert to a DataFrame
MltAsE> mylist <- list(Affy = exprmap, Methyl450k = methylmap, RNASeqGene = rnamap)

MltAsE> ## Create a sampleMap
MltAsE> mySampleMap <- listToMap(mylist)

MltAsE> ## Create an example phenotype data
MltAsE> colDat <- data.frame(sex = c("M", "F", "M", "F"),
MltAsE+                        age = 38:41,
MltAsE+                        row.names = c("Jack", "Jill", "Bob", "Barbara"))

MltAsE> ## Create a MultiAssayExperiment instance
MltAsE> myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
MltAsE+                                                colData = colDat,
MltAsE+                                                sampleMap = mySampleMap)
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 112 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 18.268   0.268  18.677

Example timings

MultiAssayExperiment.Rcheck/MultiAssayExperiment-Ex.timings

nameusersystemelapsed
API0.0040.0000.001
ExperimentList-class0.0120.0000.013
ExperimentList0.1680.0000.169
MatchedAssayExperiment-class1.1440.0201.162
MultiAssayExperiment-class1.8160.0001.818
MultiAssayExperiment-methods0.2040.0000.205
MultiAssayExperiment0.1480.0000.148
clusterOn0.4720.0040.478
hasAssay0.0040.0000.004
mapToList0.1560.0000.156
miniACC0.8840.0040.889
prepMultiAssay0.3520.0000.352
subsetBy1.6440.0081.654
upsetSamples1.9360.0121.953