| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:28 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the evaluomeR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/evaluomeR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 611/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| evaluomeR 1.11.1 (landing page) José Antonio Bernabé-Díaz
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: evaluomeR |
| Version: 1.11.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:evaluomeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings evaluomeR_1.11.1.tar.gz |
| StartedAt: 2022-03-17 19:03:03 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:06:14 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: evaluomeR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:evaluomeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings evaluomeR_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/evaluomeR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'evaluomeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'evaluomeR' version '1.11.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
'randomForest', 'flexmix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'evaluomeR' 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Namespace in Imports field not imported from: 'kableExtra'
All declared Imports should be used.
Packages in Depends field not imported from:
'flexmix' 'randomForest'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flemixModel: no visible global function definition for 'FLXMRglm'
flemixModel: no visible global function definition for 'stepFlexmix'
flemixModel: no visible global function definition for 'getModel'
globalMetric: no visible global function definition for 'prior'
metrics_pca: no visible global function definition for 'prcomp'
metrics_randomforest: no visible global function definition for
'randomForest'
metrics_randomforest: no visible global function definition for 'head'
speccCBI: no visible global function definition for 'specc'
Undefined global functions or variables:
FLXMRglm getModel head prcomp prior randomForest specc stepFlexmix
Consider adding
importFrom("stats", "prcomp")
importFrom("utils", "head")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testAll.R'
Running 'testAnalysis.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: 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/evaluomeR.Rcheck/00check.log'
for details.
evaluomeR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL evaluomeR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'evaluomeR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: evaluomeR
*** installing help indices
converting help for package 'evaluomeR'
finding HTML links ... done
bioMetrics html
evaluomeRSupportedCBI html
getDataQualityRange html
finding level-2 HTML links ... done
getOptimalKValue html
globalMetric html
metricsCorrelations html
ontMetrics html
plotMetricsBoxplot html
plotMetricsCluster html
plotMetricsClusterComparison html
plotMetricsMinMax html
plotMetricsViolin html
quality html
qualityRange html
qualitySet html
rnaMetrics html
stability html
stabilityRange html
stabilitySet html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (evaluomeR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'CNEr' is missing or broken
done
evaluomeR.Rcheck/tests/testAll.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1
Type rfNews() to see new features/changes/bug fixes.
Attaching package: 'randomForest'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: flexmix
Loading required package: lattice
>
> data("rnaMetrics")
>
> dataFrame <- stability(data=rnaMetrics, k=4, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 4
> dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,4), bs=20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
> assay(dataFrame)
Metric Mean_stability_k_2 Mean_stability_k_3 Mean_stability_k_4
[1,] "RIN" "0.825833333333333" "0.778412698412698" "0.69625"
[2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> # Metric Mean_stability_k_2 Mean_stability_k_3 Mean_stability_k_4
> # [1,] "RIN" "0.825833333333333" "0.778412698412698" "0.69625"
> # [2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> dataFrame <- stabilitySet(data=rnaMetrics, k.set=c(2,3,4), bs=20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
>
> dataFrame <- quality(data=rnaMetrics, cbi="kmeans", k=3, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Processing metric: DegFact(2)
Calculation of k = 3
> assay(dataFrame)
Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
[1,] "RIN" "0.420502645502646" "0.724044583696066" "0.68338517747747"
[2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
[1,] "0.627829396038413" "4" "4" "8"
[2,] "0.737191191352892" "8" "5" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
> # [1,] "RIN" "0.420502645502646" "0.724044583696066" "0.68338517747747"
> # [2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
> # Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # [1,] "0.627829396038413" "4" "4" "8"
> # [2,] "0.737191191352892" "8" "5" "3"
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,4), seed = 20, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
> assay(getDataQualityRange(dataFrame, 2))
Metric Cluster_1_SilScore Cluster_2_SilScore Avg_Silhouette_Width
1 "RIN" "0.583166775069983" "0.619872562681118" "0.608402004052639"
2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136"
Cluster_1_Size Cluster_2_Size
1 "5" "11"
2 "13" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Avg_Silhouette_Width Cluster_1_Size
> # 1 "RIN" "0.583166775069983" "0.619872562681118" "0.608402004052639" "5"
> # 2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136" "13"
> # Cluster_2_Size
> # 1 "11"
> # 2 "3"
> assay(getDataQualityRange(dataFrame, 4))
Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
1 "RIN" "0.420502645502646" "0.674226581940152" "0.433333333333333"
2 "DegFact" "0.759196481622952" "0.59496499852177" "0.600198799385732"
Cluster_4_SilScore Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size
1 "0.348714574898785" "0.463905611516569" "4" "4"
2 "0.521618857725795" "0.634170498361632" "5" "3"
Cluster_3_Size Cluster_4_Size
1 "3" "5"
2 "5" "3"
> # Metric Cluster_1_SilScore Cluster_2_SilScore Cluster_3_SilScore
> # 1 "RIN" "0.420502645502646" "0.674226581940152" "0.433333333333333"
> # 2 "DegFact" "0.759196481622952" "0.59496499852177" "0.600198799385732"
> # Cluster_4_SilScore Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # 1 "0.348714574898785" "0.463905611516569" "4" "4" "3"
> # 2 "0.521618857725795" "0.634170498361632" "5" "3" "5"
> # Cluster_4_Size
> # 1 "5"
> # 2 "3"
> dataFrame1 <- qualitySet(data=rnaMetrics, k.set=c(2,3,4), getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
>
>
> dataFrame <- metricsCorrelations(data=rnaMetrics, getImages = FALSE, margins = c(4,4,11,10))
Data loaded.
Number of rows: 16
Number of columns: 3
> assay(dataFrame, 1)
RIN DegFact
RIN 1.0000000 -0.9744685
DegFact -0.9744685 1.0000000
>
>
> dataFrame <- stability(data=rnaMetrics, cbi="kmeans", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara_pam", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="hclust", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk_pam", k=2, bs=100, getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Processing metric: DegFact(2)
Calculation of k = 2
>
> # Supported CBIs:
> evaluomeRSupportedCBI()
[1] "kmeans" "clara" "clara_pam" "hclust" "pamk" "pamk_pam"
>
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,10), getImages = FALSE)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
Calculation of k = 6
Calculation of k = 7
Calculation of k = 8
Calculation of k = 9
Calculation of k = 10
Processing metric: DegFact(2)
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
Calculation of k = 6
Calculation of k = 7
Calculation of k = 8
Calculation of k = 9
Calculation of k = 10
> dataFrame
ExperimentList class object of length 9:
[1] k_2: SummarizedExperiment with 2 rows and 6 columns
[2] k_3: SummarizedExperiment with 2 rows and 8 columns
[3] k_4: SummarizedExperiment with 2 rows and 10 columns
[4] k_5: SummarizedExperiment with 2 rows and 12 columns
[5] k_6: SummarizedExperiment with 2 rows and 14 columns
[6] k_7: SummarizedExperiment with 2 rows and 16 columns
[7] k_8: SummarizedExperiment with 2 rows and 18 columns
[8] k_9: SummarizedExperiment with 2 rows and 20 columns
[9] k_10: SummarizedExperiment with 2 rows and 22 columns
>
> #dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,8), bs=20, getImages = FALSE)
> #assay(dataFrame)
>
> proc.time()
user system elapsed
8.46 0.64 9.07
evaluomeR.Rcheck/tests/testAnalysis.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1
Type rfNews() to see new features/changes/bug fixes.
Attaching package: 'randomForest'
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: flexmix
Loading required package: lattice
>
> data("rnaMetrics")
> plotMetricsMinMax(rnaMetrics)
There were 17 warnings (use warnings() to see them)
> plotMetricsBoxplot(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead.
2: Use of `data.melt$value` is discouraged. Use `value` instead.
> cluster = plotMetricsCluster(ontMetrics, scale = TRUE)
> plotMetricsViolin(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead.
2: Use of `data.melt$value` is discouraged. Use `value` instead.
3: Use of `data.melt$variable` is discouraged. Use `variable` instead.
4: Use of `data.melt$value` is discouraged. Use `value` instead.
>
> stabilityData <- stabilityRange(data=rnaMetrics, k.range=c(3,4), bs=20, getImages = FALSE, seed=100)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 3
Calculation of k = 4
> qualityData <- qualityRange(data=rnaMetrics, k.range=c(3,4), getImages = FALSE, seed=100)
Data loaded.
Number of rows: 16
Number of columns: 3
Processing metric: RIN(1)
Calculation of k = 3
Calculation of k = 4
Processing metric: DegFact(2)
Calculation of k = 3
Calculation of k = 4
>
> kOptTable <- getOptimalKValue(stabilityData, qualityData, k.range=c(3,4))
Processing metric: RIN
Maximum stability and quality values matches the same K value: '3'
Processing metric: DegFact
Maximum stability and quality values matches the same K value: '3'
> kOptTable
Metric Stability_max_k Stability_max_k_stab Stability_max_k_qual
1 RIN 3 0.8901389 0.6278294
2 DegFact 3 1.0000000 0.7371912
Quality_max_k Quality_max_k_stab Quality_max_k_qual Global_optimal_k
1 3 0.8901389 0.6278294 3
2 3 1.0000000 0.7371912 3
>
>
> df = assay(rnaMetrics)
> k.vector1=rep(5,length(colnames(df))-1)
> k.vector2=rep(2,length(colnames(df))-1)
>
> plotMetricsClusterComparison(rnaMetrics, k.vector1=k.vector1, k.vector2=k.vector2)
> plotMetricsClusterComparison(rnaMetrics, k.vector1=3, k.vector2=c(2,5))
>
>
> proc.time()
user system elapsed
8.06 0.56 8.62
evaluomeR.Rcheck/evaluomeR-Ex.timings
| name | user | system | elapsed | |
| evaluomeRSupportedCBI | 0 | 0 | 0 | |
| getDataQualityRange | 0.36 | 0.01 | 0.38 | |
| getOptimalKValue | 0.25 | 0.00 | 0.25 | |
| globalMetric | 1.39 | 0.04 | 1.42 | |
| metricsCorrelations | 0.03 | 0.00 | 0.03 | |
| plotMetricsBoxplot | 0.34 | 0.04 | 0.39 | |
| plotMetricsCluster | 0.13 | 0.00 | 0.12 | |
| plotMetricsClusterComparison | 0.22 | 0.00 | 0.22 | |
| plotMetricsMinMax | 0.18 | 0.02 | 0.21 | |
| plotMetricsViolin | 0.42 | 0.03 | 0.45 | |
| quality | 0.16 | 0.03 | 0.19 | |
| qualityRange | 0.15 | 0.01 | 0.17 | |
| qualitySet | 0.05 | 0.00 | 0.05 | |
| stability | 1.59 | 0.02 | 1.61 | |
| stabilityRange | 2.04 | 0.01 | 2.04 | |
| stabilitySet | 0.36 | 0.00 | 0.36 | |