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Ignored files:
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Unstaged changes:
Modified: analysis/Identify_CNV_Regulators.Rmd
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Modified: output/cnv/dset_hnsc.RDS
Modified: output/cnv/dset_kirc.RDS
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Modified: output/cnv/regul_kirc.RDS
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Modified: output/cnv/regul_paad.RDS
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| html | f0809ae | Zhen Zuo | 2024-06-17 | . |
| Rmd | 9d7bb61 | Zhen Zuo | 2024-06-16 | . |
| html | 9d7bb61 | Zhen Zuo | 2024-06-16 | . |
| html | 15464ce | Zhen Zuo | 2024-06-16 | Build site. |
| Rmd | 9fcab2d | Zhen Zuo | 2024-06-16 | wflow_publish("*", all = TRUE) |
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library(viper)
library(EnsDb.Hsapiens.v86)
library(foreach)
library(doParallel)
cluster <- makeCluster(5)
registerDoParallel(cluster)
dir.create("output/regulon/",showWarnings = FALSE)
set.seed(0)df <- read.csv("data/KSA_gold_standard.csv")
geneID <- ensembldb::select(EnsDb.Hsapiens.v86, keys = df$UniProt.ID.1,
keytype = "UNIPROTID", columns = c("SYMBOL", "ENTREZID", "GENEID","UNIPROTID"))
df$UniProt.ID.2 <- plyr::mapvalues(df$UniProt.ID.1, from = geneID$UNIPROTID,
to = geneID$SYMBOL, warn_missing = FALSE)
df$ID <- paste(df$UniProt.ID.2,"_","S",df$Position,"_",df$seq_15, "\t", "1", sep="")
# Group by Regulator and concatenate elements of each group into strings
result <- aggregate(ID ~ Gene.name, data = df, FUN = function(x) paste(x, collapse = "\t"))
# Print the result
file <- file(paste("output/regulon/KSA_gold_standard.adj",
sep = ""))
writeLines(paste(result$Gene.name,result$ID,sep = "\t"),file)
close(file)set.seed(0)
for (name in c("kirc", "hnsc", "lusc", "luad", "paad")) {
adjfile <- "output/regulon/KSA_gold_standard.adj"
pho_normal <- readRDS(paste("output/pho/count_matrix_", name, "_normal.RDS",
sep = ""))
prot_normal <- readRDS(paste("output/prot/count_matrix_", name, "_normal.RDS",
sep = ""))
pho_tumor <- readRDS(paste("output/pho/count_matrix_", name, "_tumor.RDS",
sep = ""))
prot_tumor <- readRDS(paste("output/prot/count_matrix_", name, "_tumor.RDS",
sep = ""))
pho <- merge(pho_normal, pho_tumor, by = "row.names", all = FALSE)
prot <- merge(prot_normal, prot_tumor, by = "row.names", all = FALSE)
rownames(pho) <- pho$Row.names
pho$Row.names <- NULL
rownames(prot) <- prot$Row.names
prot$Row.names <- NULL
expr <- rbind(prot,pho)
signature <- c(rep("normal", dim(pho_normal)[2]), rep("tumor", dim(pho_tumor)[2]))
dset <- ExpressionSet(assayData = as.matrix(expr))
dset$description <- factor(signature)
regul <- aracne2regulon(adjfile, dset, verbose = TRUE)
saveRDS(dset, paste("output/pho/dset_", name, ".RDS", sep = ""))
saveRDS(regul, paste("output/pho/regul_", name, ".RDS", sep = ""))
}foreach(name = c("kirc", "hnsc", "lusc", "luad", "paad")) %dopar% {
library(viper)
dset <- readRDS(paste("output/pho/dset_", name, ".RDS",
sep = ""))
regulon <- readRDS(paste("output/pho/regul_", name, ".RDS", sep = ""))
signature <- rowTtest(dset, "description", "tumor", "normal")
signature <- (qnorm(signature$p.value/2, lower.tail = FALSE) * sign(signature$statistic))[,
1]
# NULL model by sample permutations
nullmodel <- ttestNull(dset, "description", "tumor", "normal", per = 1000,
repos = TRUE, verbose = FALSE)
## Normalized Enrichment Score (NES)
mrs <- msviper(signature, regulon, nullmodel, verbose = FALSE)
temp <- summary(mrs, length(mrs$regulon))
temp$Sign <- ifelse(temp$NES > 0, "+", "-")
temp$NES <- abs(temp$NES)
dir.create(paste("output/pho/",
name, "/", sep = ""),showWarnings = F)
write.csv(temp, paste("output/pho/",
name, "/kinase_regulators.csv", sep = ""), quote = F, sep = ",", row.names = F,
col.names = TRUE)
}[[1]]
NULL
[[2]]
NULL
[[3]]
NULL
[[4]]
NULL
[[5]]
NULL
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] doParallel_1.0.17 iterators_1.0.14
[3] foreach_1.5.2 EnsDb.Hsapiens.v86_2.99.0
[5] ensembldb_2.28.0 AnnotationFilter_1.28.0
[7] GenomicFeatures_1.56.0 AnnotationDbi_1.66.0
[9] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[11] IRanges_2.38.0 S4Vectors_0.42.0
[13] viper_1.38.0 Biobase_2.64.0
[15] BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-7
[3] rlang_1.1.4 magrittr_2.0.3
[5] git2r_0.33.0 matrixStats_1.3.0
[7] e1071_1.7-14 compiler_4.4.0
[9] RSQLite_2.3.7 png_0.1-8
[11] vctrs_0.6.5 ProtGenerics_1.36.0
[13] stringr_1.5.1 pkgconfig_2.0.3
[15] crayon_1.5.2 fastmap_1.2.0
[17] XVector_0.44.0 utf8_1.2.4
[19] Rsamtools_2.20.0 promises_1.3.0
[21] rmarkdown_2.27 UCSC.utils_1.0.0
[23] purrr_1.0.2 bit_4.0.5
[25] xfun_0.45 zlibbioc_1.50.0
[27] cachem_1.1.0 jsonlite_1.8.8
[29] blob_1.2.4 later_1.3.2
[31] DelayedArray_0.30.1 BiocParallel_1.38.0
[33] R6_2.5.1 bslib_0.7.0
[35] stringi_1.8.4 rtracklayer_1.64.0
[37] jquerylib_0.1.4 SummarizedExperiment_1.34.0
[39] Rcpp_1.0.12 knitr_1.47
[41] mixtools_2.0.0 httpuv_1.6.15
[43] Matrix_1.7-0 splines_4.4.0
[45] tidyselect_1.2.1 abind_1.4-5
[47] rstudioapi_0.16.0 yaml_2.3.8
[49] codetools_0.2-20 curl_5.2.1
[51] plyr_1.8.9 lattice_0.22-6
[53] tibble_3.2.1 KEGGREST_1.44.0
[55] evaluate_0.24.0 survival_3.7-0
[57] proxy_0.4-27 kernlab_0.9-32
[59] Biostrings_2.72.1 pillar_1.9.0
[61] MatrixGenerics_1.16.0 whisker_0.4.1
[63] KernSmooth_2.23-24 plotly_4.10.4
[65] generics_0.1.3 rprojroot_2.0.4
[67] RCurl_1.98-1.14 ggplot2_3.5.1
[69] munsell_0.5.1 scales_1.3.0
[71] class_7.3-22 glue_1.7.0
[73] lazyeval_0.2.2 tools_4.4.0
[75] BiocIO_1.14.0 data.table_1.15.4
[77] GenomicAlignments_1.40.0 fs_1.6.4
[79] XML_3.99-0.16.1 grid_4.4.0
[81] tidyr_1.3.1 colorspace_2.1-0
[83] nlme_3.1-165 GenomeInfoDbData_1.2.12
[85] restfulr_0.0.15 cli_3.6.2
[87] workflowr_1.7.1 fansi_1.0.6
[89] S4Arrays_1.4.1 segmented_2.1-0
[91] viridisLite_0.4.2 dplyr_1.1.4
[93] gtable_0.3.5 sass_0.4.9
[95] digest_0.6.35 SparseArray_1.4.8
[97] rjson_0.2.21 htmlwidgets_1.6.4
[99] memoise_2.0.1 htmltools_0.5.8.1
[101] lifecycle_1.0.4 httr_1.4.7
[103] bit64_4.0.5 MASS_7.3-61