Last updated: 2024-06-07
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Knit directory: PPP/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 69df7f0 | Zhen Zuo | 2024-06-07 | update viper pipeline |
| html | 69df7f0 | Zhen Zuo | 2024-06-07 | update viper pipeline |
| Rmd | 52f24e5 | Zhen Zuo | 2024-06-07 | add more omics |
| html | 52f24e5 | Zhen Zuo | 2024-06-07 | add more omics |
| Rmd | 97292dd | Zhen Zuo | 2024-05-31 | update rds |
| html | 97292dd | Zhen Zuo | 2024-05-31 | update rds |
library(viper)
library(aracne.networks)
library(dplyr)
library(plyr)
library(stringr)
library(Biobase)
library(EnsDb.Hsapiens.v86)
library(foreach)
library(doParallel)
dir.create("output/methy/",showWarnings = F)contains_special_characters <- function(strings) {
# Define a regular expression pattern to match special characters
pattern <- "[^A-Za-z0-9 ]"
# Check if any string in the input vector contains special
# characters
contains_special <- grepl(pattern, strings)
return(contains_special)
}df <- read.csv("data/omics_regulon_pairs.csv")for (i in 1:nrow(df)) {
exprsFile <- df$methy[i]
exprs <- as.matrix(read.table(exprsFile, header = TRUE, sep = "\t",
row.names = 1, as.is = TRUE))
rownames(exprs) <- sub("\\..*$", "", rownames(exprs))
exprs <- exprs[!duplicated(rownames(exprs)),]
geneID <- ensembldb::select(EnsDb.Hsapiens.v86, keys = rownames(exprs),
keytype = "GENEID", columns = c("SYMBOL", "ENTREZID", "GENEID"))
rownames(exprs) <- plyr::mapvalues(rownames(exprs), from = geneID$GENEID,
to = geneID$SYMBOL, warn_missing = FALSE)
exprs <- exprs[!sapply(rownames(exprs), function(x) startsWith(x, "ENSG")),
]
# Identify duplicated row names
duplicated_rows <- duplicated(rownames(exprs))
# Remove rows with duplicated row names
cleaned_exprs <- exprs[!duplicated_rows,]
cleaned_exprs <- cleaned_exprs[!contains_special_characters(rownames(cleaned_exprs)),]
saveRDS(cleaned_exprs, paste("output/methy/count_matrix_", df$Lable[i], ".RDS", sep = ""))
}
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_1.56.0 GenomeInfoDb_1.40.0
[11] IRanges_2.38.0 S4Vectors_0.42.0
[13] stringr_1.5.1 plyr_1.8.9
[15] dplyr_1.1.4 aracne.networks_1.30.0
[17] viper_1.38.0 Biobase_2.64.0
[19] BiocGenerics_0.50.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.16.0 jsonlite_1.8.8
[3] magrittr_2.0.3 rmarkdown_2.27
[5] fs_1.6.4 BiocIO_1.14.0
[7] zlibbioc_1.50.0 vctrs_0.6.5
[9] memoise_2.0.1 Rsamtools_2.20.0
[11] RCurl_1.98-1.14 htmltools_0.5.8.1
[13] S4Arrays_1.4.1 curl_5.2.1
[15] SparseArray_1.4.1 sass_0.4.9
[17] KernSmooth_2.23-24 bslib_0.7.0
[19] htmlwidgets_1.6.4 plotly_4.10.4
[21] cachem_1.1.0 GenomicAlignments_1.40.0
[23] whisker_0.4.1 lifecycle_1.0.4
[25] pkgconfig_2.0.3 Matrix_1.7-0
[27] R6_2.5.1 fastmap_1.2.0
[29] GenomeInfoDbData_1.2.12 MatrixGenerics_1.16.0
[31] digest_0.6.35 colorspace_2.1-0
[33] ps_1.7.6 rprojroot_2.0.4
[35] RSQLite_2.3.6 fansi_1.0.6
[37] httr_1.4.7 abind_1.4-5
[39] compiler_4.4.0 proxy_0.4-27
[41] bit64_4.0.5 BiocParallel_1.38.0
[43] DBI_1.2.2 MASS_7.3-60.2
[45] DelayedArray_0.30.0 rjson_0.2.21
[47] tools_4.4.0 httpuv_1.6.15
[49] glue_1.7.0 restfulr_0.0.15
[51] callr_3.7.6 nlme_3.1-164
[53] promises_1.3.0 grid_4.4.0
[55] getPass_0.2-4 generics_0.1.3
[57] gtable_0.3.5 class_7.3-22
[59] tidyr_1.3.1 data.table_1.15.4
[61] utf8_1.2.4 XVector_0.44.0
[63] pillar_1.9.0 later_1.3.2
[65] splines_4.4.0 lattice_0.22-6
[67] survival_3.6-4 rtracklayer_1.64.0
[69] bit_4.0.5 tidyselect_1.2.1
[71] Biostrings_2.72.0 knitr_1.46
[73] git2r_0.33.0 ProtGenerics_1.36.0
[75] SummarizedExperiment_1.34.0 xfun_0.44
[77] mixtools_2.0.0 matrixStats_1.3.0
[79] stringi_1.8.4 UCSC.utils_1.0.0
[81] lazyeval_0.2.2 yaml_2.3.8
[83] evaluate_0.23 codetools_0.2-20
[85] kernlab_0.9-32 tibble_3.2.1
[87] cli_3.6.2 segmented_2.1-0
[89] munsell_0.5.1 processx_3.8.4
[91] jquerylib_0.1.4 Rcpp_1.0.12
[93] png_0.1-8 XML_3.99-0.16.1
[95] ggplot2_3.5.1 blob_1.2.4
[97] bitops_1.0-7 viridisLite_0.4.2
[99] scales_1.3.0 e1071_1.7-14
[101] purrr_1.0.2 crayon_1.5.2
[103] rlang_1.1.3 KEGGREST_1.44.0