library(MethReg)
gene_exp_matrix <- read.delim("~/Downloads/input_expression_data.txt",sep = "\t")
dim(gene_exp_matrix)## [1] 17307 12head(gene_exp_matrix)## GSM2863071 GSM2863072 GSM2863073 GSM2863074 GSM2863075
## ENSG00000156508 13190.7666667 13190.76667 11521.845833 14160.815000 13515.13917
## ENSG00000111640 6895.6172500 5326.70542 5512.365333 6542.360000 7015.97858
## ENSG00000112679 -4.6590009 11.04951 -4.217649 1.910900 10.91532
## ENSG00000233927 2308.5998333 1710.36025 1964.801417 1862.215583 1593.55183
## ENSG00000117408 63.7449575 73.94238 70.652497 97.572838 61.20283
## ENSG00000196526 0.8456123 10.24920 7.390079 6.802202 2.68076
## GSM2863076 GSM2863077 GSM2863078 GSM2863079
## ENSG00000156508 13515.139167 14160.815000 13515.139167 12465.059167
## ENSG00000111640 5326.705417 7693.653083 6605.239000 7578.023250
## ENSG00000112679 4.882198 1.446334 -1.305481 3.226068
## ENSG00000233927 2108.504750 2232.658333 1828.946250 2288.409583
## ENSG00000117408 82.008979 85.909783 76.422178 113.564100
## ENSG00000196526 3.421734 1.268753 6.302435 1.759832
## GSM2863080 GSM2863081 GSM2863082
## ENSG00000156508 13190.7666667 14160.815000 14160.815000
## ENSG00000111640 5636.3837500 6895.617250 6233.255083
## ENSG00000112679 -0.2465478 4.523845 -3.572117
## ENSG00000233927 1825.2465833 1687.267167 1692.261917
## ENSG00000117408 82.3176883 85.252301 86.610962
## ENSG00000196526 4.9744703 1.802158 5.382114se <- make_exp_se(gene_exp_matrix)
se## class: RangedSummarizedExperiment
## dim: 16267 12
## metadata(1): genome
## assays(1): ''
## rownames(16267): ENSG00000156508 ENSG00000111640 ... ENSG00000221493
## ENSG00000221545
## rowData names(2): ensembl_gene_id external_gene_name
## colnames(12): GSM2863071 GSM2863072 ... GSM2863081 GSM2863082
## colData names(1): samplesSession Information
sessionInfo()## R version 4.2.0 (2022-04-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur/Monterey 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MethReg_1.7.0
##
## loaded via a namespace (and not attached):
## [1] wheatmap_0.2.0 colorspace_2.0-3
## [3] ggsignif_0.6.3 ellipsis_0.3.2
## [5] XVector_0.36.0 GenomicRanges_1.48.0
## [7] rstudioapi_0.13 ggpubr_0.4.0
## [9] bit64_4.0.5 interactiveDisplayBase_1.34.0
## [11] AnnotationDbi_1.58.0 fansi_1.0.3
## [13] codetools_0.2-18 pscl_1.5.5
## [15] cachem_1.0.6 knitr_1.39
## [17] jsonlite_1.8.0 broom_1.0.0
## [19] dbplyr_2.2.1 png_0.1-7
## [21] sfsmisc_1.1-13 shiny_1.7.1
## [23] BiocManager_1.30.18 readr_2.1.2
## [25] compiler_4.2.0 httr_1.4.3
## [27] backports_1.4.1 assertthat_0.2.1
## [29] Matrix_1.4-1 fastmap_1.1.0
## [31] cli_3.3.0 later_1.3.0
## [33] htmltools_0.5.2 prettyunits_1.1.1
## [35] tools_4.2.0 gtable_0.3.0
## [37] glue_1.6.2 GenomeInfoDbData_1.2.8
## [39] reshape2_1.4.4 dplyr_1.0.9
## [41] rappdirs_0.3.3 Rcpp_1.0.8.3
## [43] carData_3.0-5 Biobase_2.56.0
## [45] jquerylib_0.1.4 vctrs_0.4.1
## [47] Biostrings_2.64.0 preprocessCore_1.58.0
## [49] ExperimentHub_2.4.0 sesameData_1.14.0
## [51] xfun_0.31 stringr_1.4.0
## [53] mime_0.12 lifecycle_1.0.1
## [55] rstatix_0.7.0 AnnotationHub_3.4.0
## [57] zlibbioc_1.42.0 MASS_7.3-57
## [59] scales_1.2.0 hms_1.1.1
## [61] promises_1.2.0.1 MatrixGenerics_1.8.1
## [63] parallel_4.2.0 SummarizedExperiment_1.26.1
## [65] RColorBrewer_1.1-3 yaml_2.3.5
## [67] curl_4.3.2 memoise_2.0.1
## [69] ggplot2_3.3.6 sass_0.4.1
## [71] stringi_1.7.6 RSQLite_2.2.14
## [73] BiocVersion_3.15.2 S4Vectors_0.34.0
## [75] BiocGenerics_0.42.0 filelock_1.0.2
## [77] BiocParallel_1.30.3 GenomeInfoDb_1.32.2
## [79] rlang_1.0.3 pkgconfig_2.0.3
## [81] bitops_1.0-7 matrixStats_0.62.0
## [83] evaluate_0.15 sesame_1.14.2
## [85] lattice_0.20-45 purrr_0.3.4
## [87] bit_4.0.4 tidyselect_1.1.2
## [89] plyr_1.8.7 magrittr_2.0.3
## [91] R6_2.5.1 IRanges_2.30.0
## [93] generics_0.1.3 DelayedArray_0.22.0
## [95] DBI_1.1.3 pillar_1.7.0
## [97] prettydoc_0.4.1 KEGGREST_1.36.2
## [99] abind_1.4-5 RCurl_1.98-1.7
## [101] tibble_3.1.7 crayon_1.5.1
## [103] car_3.1-0 utf8_1.2.2
## [105] BiocFileCache_2.4.0 tzdb_0.3.0
## [107] rmarkdown_2.14 progress_1.2.2
## [109] grid_4.2.0 blob_1.2.3
## [111] digest_0.6.29 xtable_1.8-4
## [113] tidyr_1.2.0 httpuv_1.6.5
## [115] stats4_4.2.0 munsell_0.5.0
## [117] bslib_0.3.1