
R version 4.0.0 alpha (2020-03-31 r78116)
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Platform: x86_64-apple-darwin18.7.0 (64-bit)

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> library(spqn)
Loading required package: ggplot2
Loading required package: ggridges
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

> library(spqnData)
> library(SummarizedExperiment)
> 
> data(gtex.4k)
> cor_m <- cor(t(assay(gtex.4k)))
> ave_logrpkm <- rowData(gtex.4k)$ave_logrpkm
> 
> cor_m_spqn <- normalize_correlation(cor_m, ave_exp=ave_logrpkm, ngrp=20, size_grp=300, ref_grp=18)
> 
> cor_m_spqn_sample = cor_m_spqn[1:500,1:500]
> save(cor_m_spqn_sample, file=file.path("..", "unitTests", "cor_m_spqn_sample.rda"))
> 
> sessionInfo()
R version 4.0.0 alpha (2020-03-31 r78116)
Platform: x86_64-apple-darwin18.7.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/R/4.0/lib/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] spqnData_0.99.3             spqn_0.99.6                
 [3] SummarizedExperiment_1.17.5 DelayedArray_0.13.12       
 [5] matrixStats_0.56.0          Biobase_2.47.3             
 [7] GenomicRanges_1.39.3        GenomeInfoDb_1.23.17       
 [9] IRanges_2.21.8              S4Vectors_0.25.15          
[11] BiocGenerics_0.33.3         ggridges_0.5.2             
[13] ggplot2_3.3.0              

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6           pillar_1.4.3           compiler_4.0.0        
 [4] plyr_1.8.6             XVector_0.27.2         bitops_1.0-6          
 [7] tools_4.0.0            zlibbioc_1.33.1        lattice_0.20-40       
[10] lifecycle_0.2.0        tibble_3.0.0           gtable_0.3.0          
[13] pkgconfig_2.0.3        rlang_0.4.5            Matrix_1.2-18         
[16] cli_2.0.2              GenomeInfoDbData_1.2.3 withr_2.1.2           
[19] dplyr_0.8.5            vctrs_0.2.4            grid_4.0.0            
[22] tidyselect_1.0.0       glue_1.4.0             R6_2.4.1              
[25] fansi_0.4.1            purrr_0.3.4            magrittr_1.5          
[28] scales_1.1.0           ellipsis_0.3.0         assertthat_0.2.1      
[31] colorspace_1.4-1       RCurl_1.98-1.2         munsell_0.5.0         
[34] crayon_1.3.4          
> 
> proc.time()
   user  system elapsed 
 17.082   1.374  18.637 
