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waldronlab / MultiAssayExperiment

Bioconductor package for management of multi-assay data
https://waldronlab.io/MultiAssayExperiment/
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intersectRows() not working #202

Closed lwaldron closed 7 years ago

lwaldron commented 7 years ago 
> load("miniov.rda")
> miniov2 <- intersectRows(miniov)
> (x = rownames(miniov2))
CharacterList of length 2
[["RNASeqGene"]] AADACL3 AADACL4 ABCA4 ABCB10 ABCD3
[["RNASeq2GeneNorm"]] A1BG A1CF A2BP1 A2LD1 A2ML1
> cbind(x[[1]], x[[2]])
     [,1]      [,2]   
[1,] "AADACL3" "A1BG" 
[2,] "AADACL4" "A1CF" 
[3,] "ABCA4"   "A2BP1"
[4,] "ABCB10"  "A2LD1"
[5,] "ABCD3"   "A2ML1"
> sessionInfo()
R version 3.4.0 RC (2017-04-20 r72569)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] RaggedExperiment_1.0.0     GenomicRanges_1.28.1       GenomeInfoDb_1.12.0        IRanges_2.10.0             S4Vectors_0.14.0           Biobase_2.36.2             TCGAutils_0.3.0           
 [8] BiocGenerics_0.22.0        BiocInstaller_1.26.0       MultiAssayExperiment_1.3.5

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10               git2r_0.18.0               compiler_3.4.0             plyr_1.8.4                 XVector_0.16.0             bitops_1.0-6               tools_3.4.0               
 [8] zlibbioc_1.22.0            digest_0.6.12              jsonlite_1.4               memoise_1.1.0              tibble_1.3.0               lattice_0.20-35            Matrix_1.2-10             
[15] DelayedArray_0.2.0         shiny_1.0.3                curl_2.6                   GenomeInfoDbData_0.99.0    xml2_1.1.1                 knitr_1.15.1               httr_1.2.1                
[22] withr_1.0.2                stringr_1.2.0              hms_0.3                    devtools_1.12.0            grid_3.4.0                 shinydashboard_0.5.3       R6_2.2.1                  
[29] readr_1.1.0                reshape2_1.4.2             tidyr_0.6.2                magrittr_1.5               matrixStats_0.52.2         htmltools_0.3.6            rvest_0.3.2               
[36] SummarizedExperiment_1.6.1 mime_0.5                   xtable_1.8-2               httpuv_1.3.3               stringi_1.1.5              RCurl_1.95-4.8            
>

And sorry, I will create a good small test dataset to add to the package soon for unit testing this...

miniov.rda.zip