Abstract
Source Code
suppressPackageStartupMessages({
library(GenomicSuperSignature)
})
## Warning: package 'GenomicSuperSignature' was built under R version 4.1.3Ma et al. proposed a continuous scoring system (PCSS) based on the analysis of eight colorectal cancer microarray datasets comprising 1,867 samples, and found that PCSSs are more closely correlated to microsatellite instability (MSI), grade, stage, and tumor location.
avgLoading <- read.table("data/avg_loadings.csv",
header = TRUE, sep = ",")
avgLoading <- tibble::column_to_rownames(avgLoading, var="X")
colnames(avgLoading) <- paste0("PCSS", 1:4)
head(avgLoading)
## PCSS1 PCSS2 PCSS3 PCSS4
## A1CF -0.018923764 0.015043200 0.016192833 0.0027314229
## A2M 0.022619204 0.016479342 0.008791011 -0.0007293910
## AAAS -0.002700998 -0.005051213 -0.001248883 0.0037994266
## AACS -0.002542282 -0.006858940 0.005834412 0.0058956790
## AADAC -0.003473766 -0.002360232 -0.003660762 -0.0047612188
## AAK1 0.001522205 0.005908014 -0.004708509 -0.0006853461
RAVmodel <- getModel("C2", load=TRUE)
RAVmodel
## class: PCAGenomicSignatures
## dim: 13934 4764
## metadata(8): cluster size ... version geneSets
## assays(1): RAVindex
## rownames(13934): CASKIN1 DDX3Y ... CTC-457E21.9 AC007966.1
## rowData names(0):
## colnames(4764): RAV1 RAV2 ... RAV4763 RAV4764
## colData names(4): RAV studies silhouetteWidth gsea
## trainingData(2): PCAsummary MeSH
## trainingData names(536): DRP000987 SRP059172 ... SRP164913 SRP188526
version(RAVmodel)
## [1] "1.1.1"We identified RAV1575 and RAV834 as the most similar RAVs to PCSS1 and PCSS2, respectively, based on Pearson correlation coefficient.
cg <- intersect(rownames(avgLoading), rownames(RAVmodel))
loading_cor <- abs(stats::cor(avgLoading[cg,], RAVindex(RAVmodel)[cg,],
use="pairwise.complete.obs", method="pearson"))
max1 <- which.max(loading_cor[1,]) # max. correlation with PCSS1
max2 <- which.max(loading_cor[2,]) # max. correlation with PCSS2
loading_cor[1, max1, drop = FALSE]
## RAV1575
## PCSS1 0.5894306
loading_cor[2, max2, drop = FALSE]
## RAV834
## PCSS2 0.5624299
sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] GenomicSuperSignature_1.3.6 SummarizedExperiment_1.24.0
## [3] Biobase_2.54.0 GenomicRanges_1.46.1
## [5] GenomeInfoDb_1.30.1 IRanges_2.28.0
## [7] S4Vectors_0.32.3 BiocGenerics_0.40.0
## [9] MatrixGenerics_1.6.0 matrixStats_0.61.0
## [11] BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 fs_1.5.2 bit64_4.0.5
## [4] filelock_1.0.2 httr_1.4.2 doParallel_1.0.17
## [7] RColorBrewer_1.1-2 rprojroot_2.0.2 tools_4.1.2
## [10] backports_1.4.1 bslib_0.3.1 utf8_1.2.2
## [13] R6_2.5.1 DBI_1.1.2 colorspace_2.0-3
## [16] GetoptLong_1.0.5 tidyselect_1.1.2 curl_4.3.2
## [19] bit_4.0.4 compiler_4.1.2 textshaping_0.3.6
## [22] cli_3.2.0 desc_1.4.1 DelayedArray_0.20.0
## [25] bookdown_0.25 sass_0.4.0 scales_1.1.1
## [28] rappdirs_0.3.3 pkgdown_2.0.2 systemfonts_1.0.4
## [31] stringr_1.4.0 digest_0.6.29 rmarkdown_2.13
## [34] XVector_0.34.0 pkgconfig_2.0.3 htmltools_0.5.2
## [37] dbplyr_2.1.1 fastmap_1.1.0 rlang_1.0.2
## [40] GlobalOptions_0.1.2 RSQLite_2.2.10 shape_1.4.6
## [43] jquerylib_0.1.4 generics_0.1.2 jsonlite_1.8.0
## [46] dplyr_1.0.8 car_3.0-12 RCurl_1.98-1.6
## [49] magrittr_2.0.2 GenomeInfoDbData_1.2.7 Matrix_1.4-0
## [52] Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.2
## [55] abind_1.4-5 lifecycle_1.0.1 stringi_1.7.6
## [58] yaml_2.3.5 carData_3.0-5 zlibbioc_1.40.0
## [61] BiocFileCache_2.2.1 blob_1.2.2 grid_4.1.2
## [64] parallel_4.1.2 crayon_1.5.0 lattice_0.20-45
## [67] circlize_0.4.14 knitr_1.37 ComplexHeatmap_2.10.0
## [70] pillar_1.7.0 ggpubr_0.4.0 rjson_0.2.21
## [73] ggsignif_0.6.3 codetools_0.2-18 glue_1.6.2
## [76] evaluate_0.15 BiocManager_1.30.16 png_0.1-7
## [79] vctrs_0.3.8 foreach_1.5.2 gtable_0.3.0
## [82] purrr_0.3.4 tidyr_1.2.0 clue_0.3-60
## [85] assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5
## [88] xfun_0.30 broom_0.7.12 rstatix_0.7.0
## [91] ragg_1.2.2 tibble_3.1.6 iterators_1.0.14
## [94] memoise_2.0.1 cluster_2.1.2 ellipsis_0.3.2