Last updated: 2023-01-18
Checks: 5 1
Knit directory:
LungCancer_SotilloLab/analysis/
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Packages
#package
library(SummarizedExperiment)
library(MultiAssayExperiment)
library(proDA)
library(UpSetR)
library(tidyverse)
source("../code/utils.R")
knitr::opts_chunk$set(warning = FALSE, message = FALSE, autodep = TRUE)Preprocessed data
load("../output/processedData_RUN5.RData")
#load saved result list
load("../output/allResList_RUN5_timeBased.RData")
#a list to collect all results
#allResList <- list()We hypothesize that dasatinib is inhibiting other proteins apart from SRC. Check the status (global/phospho) of the described off targets in dasatinib or combo treated cells: ABL1, ABL2, BLK, EPHA2, FGR, FRK, FYN, HCK, KIT, LCK, LYN, PDGFRB, SRC, SRMS, STAT5B, YES1, EGFR
geneList <- sort(c("Abl1", "Abl2", "Blk", "Epha2", "Fgr", "Frk", "Fyn",
"Hck", "Kit", "Lck", "Lyn", "Pdgfrb", "Src", "Srms", "Stat5b", "Yes1", "Egfr","Akt1","Akt2","Akt3",
"Stat1","Stat3","Stat5a","Stat5b","Mapk1","Mapk3","Mapk4","Pik3ca","Pik3cb","Pik3c3","Pik3c2a",
"Pik3r2","Pik3r1","Pik3c2g","Jak1","Rasa1","Rasa2","Rasa3","Rhoa","Rhob","Rhoc","Rhog","Rhod"))Proteome
fpeSub <- preprocessProteome(maeData, filterList = list(drug =c("brigatinib","dasatinib","DMSO")), missCut = 1, transform = "vst", normalize = TRUE)[1] "Number of proteins and samples:"
[1] 8028 66fpeDMSO <- fpeSub[,fpeSub$drug=="DMSO"]
fpeBri0 <- fpeDMSO
colnames(fpeBri0) <- str_replace(colnames(fpeBri0),"DMSO","dasatinib")
fpeBri0$drug <- "dasatinib"
#0 time for brigatinib
fpeCombo0 <- fpeDMSO
colnames(fpeCombo0) <- str_replace(colnames(fpeCombo0),"DMSO","brigatinib")
fpeCombo0$drug <- "brigatinib"
#combine a new fpe data
fpeDrug <- fpeSub[,fpeSub$drug!="DMSO"]
fpeNew <- cbind(fpeDrug, fpeBri0, fpeCombo0)Phosphoproteome
ppeSub <- preprocessPhos(maeData, filterList = list(drug =c("dasatinib","brigatinib","DMSO")),
missCut = 1, transform = "vst", normalize = TRUE)[1] "Number of proteins and samples:"
[1] 19619 66ppeDMSO <- ppeSub[,ppeSub$drug=="DMSO"]
#0 time for dasatinib
ppeBri0 <- ppeDMSO
colnames(ppeBri0) <- str_replace(colnames(ppeBri0),"DMSO","dasatinib")
ppeBri0$drug <- "dasatinib"
#0 time for brigatinib
ppeCombo0 <- ppeDMSO
colnames(ppeCombo0) <- str_replace(colnames(ppeCombo0),"DMSO","brigatinib")
ppeCombo0$drug <- "brigatinib"
#combine a new ppe data
ppeDrug <- ppeSub[,ppeSub$drug!="DMSO"]
ppeNew <- cbind(ppeDrug, ppeBri0, ppeCombo0)Create plots
pList <- plotPhosProt(geneList, fpeNew, ppeNew, averageReplicate = TRUE)jyluMisc::makepdf(pList, "../docs/Dasatinib_effect_RUN5.pdf", ncol = 1, nrow=3, height = 20, width = 12)
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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] forcats_0.5.1 stringr_1.4.1
[3] dplyr_1.0.9 purrr_0.3.4
[5] readr_2.1.2 tidyr_1.2.0
[7] tibble_3.1.8 ggplot2_3.3.6
[9] tidyverse_1.3.2 UpSetR_1.4.0
[11] proDA_1.10.0 MultiAssayExperiment_1.22.0
[13] SummarizedExperiment_1.26.1 Biobase_2.56.0
[15] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[17] IRanges_2.30.0 S4Vectors_0.34.0
[19] BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[21] matrixStats_0.62.0
loaded via a namespace (and not attached):
[1] DEP_1.18.0 utf8_1.2.2 shinydashboard_0.7.2
[4] gmm_1.6-6 tidyselect_1.1.2 htmlwidgets_1.5.4
[7] grid_4.2.0 BiocParallel_1.30.3 norm_1.0-10.0
[10] maxstat_0.7-25 munsell_0.5.0 codetools_0.2-18
[13] preprocessCore_1.58.0 DT_0.23 withr_2.5.0
[16] colorspace_2.0-3 knitr_1.39 rstudioapi_0.13
[19] ggsignif_0.6.3 mzID_1.34.0 git2r_0.30.1
[22] slam_0.1-50 GenomeInfoDbData_1.2.8 KMsurv_0.1-5
[25] rprojroot_2.0.3 vctrs_0.4.1 generics_0.1.3
[28] TH.data_1.1-1 xfun_0.31 sets_1.0-21
[31] R6_2.5.1 doParallel_1.0.17 clue_0.3-61
[34] MsCoreUtils_1.8.0 fgsea_1.22.0 bitops_1.0-7
[37] cachem_1.0.6 DelayedArray_0.22.0 assertthat_0.2.1
[40] promises_1.2.0.1 scales_1.2.0 multcomp_1.4-19
[43] googlesheets4_1.0.0 gtable_0.3.0 affy_1.74.0
[46] sandwich_3.0-2 workflowr_1.7.0 rlang_1.0.6
[49] mzR_2.30.0 GlobalOptions_0.1.2 splines_4.2.0
[52] rstatix_0.7.0 gargle_1.2.0 impute_1.70.0
[55] broom_1.0.0 BiocManager_1.30.18 yaml_2.3.5
[58] abind_1.4-5 modelr_0.1.8 backports_1.4.1
[61] httpuv_1.6.6 tools_4.2.0 relations_0.6-12
[64] affyio_1.66.0 ellipsis_0.3.2 gplots_3.1.3
[67] jquerylib_0.1.4 RColorBrewer_1.1-3 MSnbase_2.22.0
[70] Rcpp_1.0.9 plyr_1.8.7 visNetwork_2.1.0
[73] zlibbioc_1.42.0 RCurl_1.98-1.7 ggpubr_0.4.0
[76] GetoptLong_1.0.5 cowplot_1.1.1 zoo_1.8-10
[79] haven_2.5.0 cluster_2.1.3 exactRankTests_0.8-35
[82] fs_1.5.2 magrittr_2.0.3 data.table_1.14.2
[85] circlize_0.4.15 survminer_0.4.9 reprex_2.0.1
[88] googledrive_2.0.0 pcaMethods_1.88.0 mvtnorm_1.1-3
[91] ProtGenerics_1.28.0 shinyjs_2.1.0 hms_1.1.1
[94] mime_0.12 evaluate_0.15 xtable_1.8-4
[97] XML_3.99-0.10 readxl_1.4.0 gridExtra_2.3
[100] shape_1.4.6 compiler_4.2.0 KernSmooth_2.23-20
[103] ncdf4_1.19 crayon_1.5.2 htmltools_0.5.3
[106] later_1.3.0 tzdb_0.3.0 lubridate_1.8.0
[109] DBI_1.1.3 dbplyr_2.2.1 ComplexHeatmap_2.12.0
[112] MASS_7.3-58 tmvtnorm_1.5 jyluMisc_0.1.5
[115] Matrix_1.4-1 car_3.1-0 cli_3.4.1
[118] vsn_3.64.0 imputeLCMD_2.1 marray_1.74.0
[121] parallel_4.2.0 igraph_1.3.4 km.ci_0.5-6
[124] pkgconfig_2.0.3 piano_2.12.0 MALDIquant_1.21
[127] xml2_1.3.3 foreach_1.5.2 bslib_0.4.1
[130] XVector_0.36.0 drc_3.0-1 rvest_1.0.2
[133] digest_0.6.30 fastmatch_1.1-3 rmarkdown_2.14
[136] cellranger_1.1.0 survMisc_0.5.6 shiny_1.7.3
[139] gtools_3.9.3 rjson_0.2.21 lifecycle_1.0.3
[142] jsonlite_1.8.3 carData_3.0-5 limma_3.52.2
[145] fansi_1.0.3 pillar_1.8.0 lattice_0.20-45
[148] fastmap_1.1.0 httr_1.4.3 plotrix_3.8-2
[151] survival_3.4-0 glue_1.6.2 png_0.1-7
[154] iterators_1.0.14 stringi_1.7.8 sass_0.4.2
[157] caTools_1.18.2