1. download data
## WARNING: cannot verify costalab.ukaachen.de's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
## Unable to locally verify the issuer's authority.
## 2024-10-23 12:32:07 URL:https://costalab.ukaachen.de/open_data/MOJITOO/ATAC_LSI.Rds [1380864/1380864] -> "ATAC_LSI.Rds" [1]
## WARNING: cannot verify costalab.ukaachen.de's certificate, issued by ‘CN=GEANT OV RSA CA 4,O=GEANT Vereniging,C=NL’:
## Unable to locally verify the issuer's authority.
## 2024-10-23 12:32:08 URL:https://costalab.ukaachen.de/open_data/MOJITOO/RNA_PCA.Rds [1390391/1390391] -> "RNA_PCA.Rds" [1]
3. LOADING DATA
RNA_PCA = readRDS("RNA_PCA.Rds")
ATAC_LSI = readRDS("ATAC_LSI.Rds")
(RNA_PCA[1:5, 1:5])
## PC_1 PC_2 PC_3 PC_4 PC_5
## ACCTTCCAGGAACGCG-1 -18.722372 3.2061442 -4.427158 -1.6254263 -10.133467
## GGTTCTTGTCCTTAGT-1 -14.447415 0.6859972 5.093509 7.8732573 21.056898
## CGTATTGCATTCAGCA-1 9.753255 2.4812830 -4.249865 -3.2154207 1.495905
## TGAGGCACAACAGGTG-1 -17.249908 1.8702171 -2.040451 0.4033981 -1.186289
## TCACGGATCTCACAAA-1 6.555031 -14.9040450 1.280343 0.5568495 -2.309631
## LSI_1 LSI_2 LSI_3 LSI_4 LSI_5
## ACCTTCCAGGAACGCG-1 -0.3456660 -1.2187188 -0.29848099 0.07280032 -0.16058723
## GGTTCTTGTCCTTAGT-1 -0.9354829 -1.6351802 0.01148662 0.04542933 -0.01966307
## CGTATTGCATTCAGCA-1 0.0485317 0.8786845 -0.40229951 0.88748465 0.46213190
## TGAGGCACAACAGGTG-1 -0.7041392 -1.2302514 -0.09467401 0.14793960 0.11523086
## TCACGGATCTCACAAA-1 -0.4350341 0.2969706 2.61745329 -0.28567776 0.47715209
## dims of pca & lsi: 3536 50, 3536 50
4. RUN MOJITOO
MOJITOO_DM <- mojitoo_Matrix(
reduction_matrix.list= list(RNA_PCA, ATAC_LSI),
dims.list = list(1:50, 2:50) ## exclude 1st dimension of LSI
)
## processing 1
## adding 2
## 1 round cc 44
## mojitoo1 mojitoo2 mojitoo3 mojitoo4 mojitoo5
## ACCTTCCAGGAACGCG-1 0.3041858 2.62861275 -0.6237414 0.5587585 -2.6407216
## GGTTCTTGTCCTTAGT-1 0.7631513 3.59702871 -0.4402510 -0.2070474 10.6965888
## CGTATTGCATTCAGCA-1 0.2236081 -2.02918067 -0.7249151 1.5748186 0.6869435
## TGAGGCACAACAGGTG-1 0.2447969 2.87887439 -0.5511696 0.2130495 -0.3620080
## TCACGGATCTCACAAA-1 -3.2072954 -0.08991125 3.4165403 -0.1093769 -0.2516832
## dims of MOJITOO_DM: 3536 44
SessionInfo
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-conda-linux-gnu (64-bit)
## Running under: Rocky Linux 8.10 (Green Obsidian)
##
## Matrix products: default
## BLAS/LAPACK: /data/sz753404/miniconda3/envs/schema/lib/libopenblasp-r0.3.21.so
##
## locale:
## [1] LC_CTYPE=en_US.utf-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.utf-8
## [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.utf-8
## [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MOJITOO_1.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 rtracklayer_1.52.1
## [3] scattermore_0.8 SeuratObject_4.1.3
## [5] ragg_1.3.3 tidyr_1.2.1
## [7] ggplot2_3.4.1 bit64_4.0.5
## [9] knitr_1.42 irlba_2.3.5.1
## [11] DelayedArray_0.18.0 data.table_1.14.8
## [13] rpart_4.1.19 KEGGREST_1.34.0
## [15] RCurl_1.98-1.10 AnnotationFilter_1.16.0
## [17] doParallel_1.0.16 generics_0.1.3
## [19] BiocGenerics_0.40.0 GenomicFeatures_1.44.2
## [21] cowplot_1.1.1 RSQLite_2.3.0
## [23] RANN_2.6.1 future_1.28.0
## [25] bit_4.0.5 spatstat.data_3.0-0
## [27] xml2_1.3.3 httpuv_1.6.5
## [29] SummarizedExperiment_1.22.0 assertthat_0.2.1
## [31] xfun_0.37 hms_1.1.2
## [33] jquerylib_0.1.4 evaluate_0.20
## [35] promises_1.2.0.1 fansi_1.0.4
## [37] restfulr_0.0.13 progress_1.2.2
## [39] dbplyr_2.3.1 igraph_1.4.1
## [41] DBI_1.1.3 htmlwidgets_1.6.1
## [43] spatstat.geom_3.0-3 stats4_4.1.0
## [45] purrr_1.0.1 ellipsis_0.3.2
## [47] ks_1.13.3 dplyr_1.1.0
## [49] backports_1.4.1 biomaRt_2.48.3
## [51] deldir_1.0-6 MatrixGenerics_1.4.3
## [53] vctrs_0.5.2 Biobase_2.54.0
## [55] here_1.0.1 ensembldb_2.16.4
## [57] ROCR_1.0-11 abind_1.4-5
## [59] cachem_1.0.7 Gviz_1.36.2
## [61] BSgenome_1.60.0 progressr_0.10.1
## [63] checkmate_2.1.0 sctransform_0.3.5
## [65] GenomicAlignments_1.28.0 prettyunits_1.1.1
## [67] mclust_5.4.9 goftest_1.2-3
## [69] cluster_2.1.4 lazyeval_0.2.2
## [71] crayon_1.5.2 spatstat.explore_3.0-5
## [73] pkgconfig_2.0.3 GenomeInfoDb_1.30.1
## [75] nlme_3.1-160 ProtGenerics_1.26.0
## [77] nnet_7.3-18 rlang_1.0.6
## [79] globals_0.16.1 lifecycle_1.0.3
## [81] miniUI_0.1.1.1 filelock_1.0.2
## [83] BiocFileCache_2.0.0 dichromat_2.0-0.1
## [85] rprojroot_2.0.3 polyclip_1.10-4
## [87] matrixStats_0.62.0 lmtest_0.9-40
## [89] Matrix_1.5-3 Rhdf5lib_1.16.0
## [91] zoo_1.8-10 base64enc_0.1-3
## [93] ggridges_0.5.3 GlobalOptions_0.1.2
## [95] png_0.1-8 viridisLite_0.4.1
## [97] rjson_0.2.20 bitops_1.0-7
## [99] KernSmooth_2.23-20 rhdf5filters_1.4.0
## [101] Biostrings_2.62.0 blob_1.2.3
## [103] shape_1.4.6 stringr_1.5.0
## [105] parallelly_1.32.1 spatstat.random_3.0-1
## [107] jpeg_0.1-9 S4Vectors_0.32.4
## [109] scales_1.2.1 memoise_2.0.1
## [111] magrittr_2.0.3 plyr_1.8.8
## [113] ica_1.0-3 zlibbioc_1.40.0
## [115] hdrcde_3.4 compiler_4.1.0
## [117] BiocIO_1.2.0 RColorBrewer_1.1-3
## [119] clue_0.3-60 fitdistrplus_1.1-8
## [121] Rsamtools_2.8.0 cli_3.6.0
## [123] XVector_0.34.0 listenv_0.8.0
## [125] patchwork_1.1.2 pbapply_1.7-0
## [127] htmlTable_2.3.0 Formula_1.2-4
## [129] MASS_7.3-58.1 tidyselect_1.2.0
## [131] stringi_1.7.12 textshaping_0.3.6
## [133] yaml_2.3.7 latticeExtra_0.6-29
## [135] ggrepel_0.9.3 grid_4.1.0
## [137] sass_0.4.5 VariantAnnotation_1.38.0
## [139] tools_4.1.0 future.apply_1.9.0
## [141] parallel_4.1.0 circlize_0.4.13
## [143] rstudioapi_0.14 foreach_1.5.2
## [145] foreign_0.8-84 gridExtra_2.3
## [147] Rtsne_0.16 digest_0.6.31
## [149] pracma_2.3.8 shiny_1.7.2
## [151] Rcpp_1.0.10 GenomicRanges_1.44.0
## [153] later_1.3.0 RcppAnnoy_0.0.19
## [155] fda_5.5.1 httr_1.4.5
## [157] AnnotationDbi_1.56.2 biovizBase_1.40.0
## [159] ComplexHeatmap_2.11.1 colorspace_2.1-0
## [161] XML_3.99-0.13 fs_1.6.1
## [163] tensor_1.5 rainbow_3.6
## [165] reticulate_1.25 IRanges_2.28.0
## [167] splines_4.1.0 uwot_0.1.14
## [169] spatstat.utils_3.1-0 pkgdown_2.0.3
## [171] sp_1.5-1 ArchR_1.0.1
## [173] plotly_4.10.1 systemfonts_1.0.4
## [175] xtable_1.8-4 jsonlite_1.8.4
## [177] fds_1.8 corpcor_1.6.10
## [179] R6_2.5.1 Hmisc_5.0-1
## [181] ramify_0.3.3 pillar_1.8.1
## [183] htmltools_0.5.4 mime_0.12
## [185] glue_1.6.2 fastmap_1.1.1
## [187] BiocParallel_1.28.3 deSolve_1.32
## [189] codetools_0.2-19 pcaPP_2.0-1
## [191] mvtnorm_1.1-3 utf8_1.2.3
## [193] lattice_0.20-45 bslib_0.4.2
## [195] spatstat.sparse_3.0-0 tibble_3.2.0
## [197] curl_5.0.0 leiden_0.4.2
## [199] survival_3.5-5 rmarkdown_2.20
## [201] desc_1.4.2 munsell_0.5.0
## [203] GetoptLong_1.0.5 rhdf5_2.36.0
## [205] GenomeInfoDbData_1.2.7 iterators_1.0.14
## [207] reshape2_1.4.4 gtable_0.3.1
## [209] Seurat_4.3.0
