Show the Annotations of a signature object
Source:R/class-SignatureClass.R
showSigAnnot-PharmacoSig-method.RdThis funtion prints out the information about the call used to compute the drug signatures, and the session info for the session in which the computation was done. Useful for determining the exact conditions used to generate signatures.
Arguments
- object
An object of the
PharmacoSigClass, as returned bydrugPerturbationSigordrugSensitivitySig
Value
Prints the PharmacoGx Signatures annotations to the output stream, and returns invisible NULL.
Examples
data(GDSCsmall)
drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna",
nthread=1, features = fNames(GDSCsmall, "rna")[1])
#> Summarizing rna molecular data for: GDSC
#>
|
| | 0%
|
|======================================================================| 100%
#> Computing drug sensitivity signatures...
showSigAnnot(drug.sensitivity)
#> [1] ".drugSensitivitySigPharmacoSet" "object"
#> [3] "mDataType" "drugs"
#> [5] "features" "cells"
#> [7] "tissues" "sensitivity.measure"
#> [9] "molecular.summary.stat" "sensitivity.summary.stat"
#> [11] "returnValues" "sensitivity.cutoff"
#> [13] "standardize" "molecular.cutoff"
#> [15] "molecular.cutoff.direction" "nthread"
#> [17] "parallel.on" "modeling.method"
#> [19] "inference.method" "verbose"
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
#>
#> locale:
#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] PharmacoGx_3.7.5 CoreGx_2.2.0
#> [3] SummarizedExperiment_1.28.0 Biobase_2.58.0
#> [5] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
#> [7] IRanges_2.32.0 S4Vectors_0.36.2
#> [9] MatrixGenerics_1.10.0 matrixStats_1.3.0
#> [11] BiocGenerics_0.44.0
#>
#> loaded via a namespace (and not attached):
#> [1] fgsea_1.24.0 colorspace_2.1-0
#> [3] lsa_0.73.3 XVector_0.38.0
#> [5] fs_1.6.3 farver_2.1.1
#> [7] SnowballC_0.7.1 MultiAssayExperiment_1.24.0
#> [9] DT_0.33 fansi_1.0.6
#> [11] xml2_1.3.6 codetools_0.2-18
#> [13] downlit_0.4.3 cachem_1.0.8
#> [15] knitr_1.46 jsonlite_1.8.8
#> [17] cluster_2.1.3 shinydashboard_0.7.2
#> [19] shiny_1.8.1.1 compiler_4.2.1
#> [21] httr_1.4.7 backports_1.4.1
#> [23] Matrix_1.4-1 fastmap_1.1.1
#> [25] bench_1.1.3 limma_3.54.2
#> [27] cli_3.6.2 later_1.3.2
#> [29] visNetwork_2.1.2 htmltools_0.5.8.1
#> [31] tools_4.2.1 igraph_2.0.3
#> [33] gtable_0.3.4 glue_1.7.0
#> [35] GenomeInfoDbData_1.2.9 reshape2_1.4.4
#> [37] dplyr_1.1.4 fastmatch_1.1-4
#> [39] Rcpp_1.0.12 slam_0.1-50
#> [41] jquerylib_0.1.4 pkgdown_2.0.8
#> [43] vctrs_0.6.5 BumpyMatrix_1.6.0
#> [45] xfun_0.43 stringr_1.5.1
#> [47] mime_0.12 lifecycle_1.0.4
#> [49] gtools_3.9.5 zlibbioc_1.44.0
#> [51] scales_1.3.0 ragg_1.3.0
#> [53] promises_1.3.0 relations_0.6-13
#> [55] parallel_4.2.1 RColorBrewer_1.1-3
#> [57] sets_1.0-25 yaml_2.3.8
#> [59] curl_5.2.1 memoise_2.0.1
#> [61] ggplot2_3.5.0 downloader_0.4
#> [63] sass_0.4.9 stringi_1.8.3
#> [65] desc_1.4.3 checkmate_2.3.1
#> [67] caTools_1.18.2 boot_1.3-28
#> [69] BiocParallel_1.32.6 rlang_1.1.3
#> [71] pkgconfig_2.0.3 systemfonts_1.0.6
#> [73] bitops_1.0-7 evaluate_0.23
#> [75] lattice_0.20-45 purrr_1.0.2
#> [77] labeling_0.4.3 htmlwidgets_1.6.4
#> [79] cowplot_1.1.3 tidyselect_1.2.1
#> [81] plyr_1.8.9 magrittr_2.0.3
#> [83] R6_2.5.1 gplots_3.1.3.1
#> [85] generics_0.1.3 DelayedArray_0.24.0
#> [87] pillar_1.9.0 whisker_0.4.1
#> [89] withr_3.0.0 RCurl_1.98-1.14
#> [91] tibble_3.2.1 crayon_1.5.2
#> [93] KernSmooth_2.23-20 utf8_1.2.4
#> [95] rmarkdown_2.26 grid_4.2.1
#> [97] data.table_1.15.4 marray_1.76.0
#> [99] piano_2.14.0 digest_0.6.35
#> [101] xtable_1.8-4 httpuv_1.6.15
#> [103] BiocBaseUtils_1.0.0 textshaping_0.3.7
#> [105] coop_0.6-3 munsell_0.5.1
#> [107] bslib_0.7.0 shinyjs_2.1.0