Run_all_analysis
ERM
20230410
Last updated: 2023-04-10
Checks: 7 0
Knit directory: Cardiotoxicity/
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| Rmd | 1444a85 | reneeisnowhere | 2023-04-10 | update push of new data |
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This starts the documentation of the RNA-seq cardiotoxicity analysis for my manuscript
library(edgeR)#
library(limma)#
library(RColorBrewer)
library(mixOmics)
library(gridExtra)#
library(reshape2)#
#library(devtools)
library(AnnotationHub)
library(tidyverse)
library(scales)
library(biomaRt)#
library(Homo.sapiens)
library(cowplot)#
library(ggrepel)#
library(corrplot)
library(Hmisc) ###now we add genenames to the geneid###
geneid <- rownames(mymatrix) ### pulls the names we have in the counts file
genes <- select(Homo.sapiens, keys=geneid, columns=c("SYMBOL"),
keytype="ENTREZID")
genes <- genes[!duplicated(genes$ENTREZID),]
mymatrix$genes <- genes[1] 28395 72[1] 14086 72
### Vehicle 
### Daunorubicin 
### Doxorubicin 
### Epirubicin 
### Mitoxantrone 
### Trastuzumab 
samplenames indv drug time RIN group PC1 PC2
Da.1.3h MCW_RM_R_11 1 Daunorubicin 3h 9.3 1 -18.53902 62.11914
Do.1.3h MCW_RM_R_12 1 Doxorubicin 3h 9.8 2 -12.37874 73.96424
Ep.1.3h MCW_RM_R_13 1 Epirubicin 3h 9.8 3 -11.19226 66.47554
Mi.1.3h MCW_RM_R_14 1 Mitoxantrone 3h 10 4 -10.24538 73.46900
Tr.1.3h MCW_RM_R_15 1 Trastuzumab 3h 9.6 5 -12.21578 79.97646
Ve.1.3h MCW_RM_R_16 1 Vehicle 3h 9.9 6 -15.01396 76.61739
PC3 PC4 PC5 PC6
Da.1.3h 44.793907 -4.229684 25.33474 -35.96203
Do.1.3h 24.565270 -8.522490 -19.86738 -19.00810
Ep.1.3h 33.103318 -9.146883 18.17321 -43.12911
Mi.1.3h 19.048074 -14.540036 -9.00047 -24.33769
Tr.1.3h 2.646249 -17.004856 -34.18428 -11.83222
Ve.1.3h 12.636907 -4.140009 -39.84065 -17.16481
##correlation heatmap of counts matrix
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Hmisc_4.8-0
[2] Formula_1.2-5
[3] survival_3.5-3
[4] corrplot_0.92
[5] ggrepel_0.9.3
[6] cowplot_1.1.1
[7] Homo.sapiens_1.3.1
[8] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[9] org.Hs.eg.db_3.15.0
[10] GO.db_3.15.0
[11] OrganismDbi_1.38.1
[12] GenomicFeatures_1.48.4
[13] GenomicRanges_1.48.0
[14] GenomeInfoDb_1.32.4
[15] AnnotationDbi_1.58.0
[16] IRanges_2.30.1
[17] S4Vectors_0.34.0
[18] Biobase_2.56.0
[19] biomaRt_2.52.0
[20] scales_1.2.1
[21] lubridate_1.9.2
[22] forcats_1.0.0
[23] stringr_1.5.0
[24] dplyr_1.1.0
[25] purrr_1.0.1
[26] readr_2.1.4
[27] tidyr_1.3.0
[28] tibble_3.1.8
[29] tidyverse_2.0.0
[30] AnnotationHub_3.4.0
[31] BiocFileCache_2.4.0
[32] dbplyr_2.3.1
[33] BiocGenerics_0.42.0
[34] reshape2_1.4.4
[35] gridExtra_2.3
[36] mixOmics_6.20.0
[37] ggplot2_3.4.1
[38] lattice_0.20-45
[39] MASS_7.3-58.2
[40] RColorBrewer_1.1-3
[41] edgeR_3.38.4
[42] limma_3.52.4
[43] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] backports_1.4.1 plyr_1.8.8
[3] igraph_1.4.1 splines_4.2.2
[5] BiocParallel_1.30.4 digest_0.6.31
[7] htmltools_0.5.4 fansi_1.0.4
[9] checkmate_2.1.0 magrittr_2.0.3
[11] memoise_2.0.1 cluster_2.1.4
[13] tzdb_0.3.0 Biostrings_2.64.1
[15] matrixStats_0.63.0 rARPACK_0.11-0
[17] timechange_0.2.0 prettyunits_1.1.1
[19] jpeg_0.1-10 colorspace_2.1-0
[21] blob_1.2.3 rappdirs_0.3.3
[23] xfun_0.37 callr_3.7.3
[25] crayon_1.5.2 RCurl_1.98-1.10
[27] jsonlite_1.8.4 graph_1.74.0
[29] glue_1.6.2 gtable_0.3.1
[31] zlibbioc_1.42.0 XVector_0.36.0
[33] DelayedArray_0.22.0 pheatmap_1.0.12
[35] DBI_1.1.3 Rcpp_1.0.10
[37] htmlTable_2.4.1 xtable_1.8-4
[39] progress_1.2.2 foreign_0.8-84
[41] bit_4.0.5 htmlwidgets_1.6.1
[43] httr_1.4.5 ellipsis_0.3.2
[45] farver_2.1.1 pkgconfig_2.0.3
[47] XML_3.99-0.13 nnet_7.3-18
[49] deldir_1.0-6 sass_0.4.5
[51] locfit_1.5-9.7 utf8_1.2.3
[53] labeling_0.4.2 tidyselect_1.2.0
[55] rlang_1.0.6 later_1.3.0
[57] munsell_0.5.0 BiocVersion_3.15.2
[59] tools_4.2.2 cachem_1.0.7
[61] cli_3.6.0 generics_0.1.3
[63] RSQLite_2.3.0 evaluate_0.20
[65] fastmap_1.1.1 yaml_2.3.7
[67] processx_3.8.0 knitr_1.42
[69] bit64_4.0.5 fs_1.6.1
[71] KEGGREST_1.36.3 RBGL_1.72.0
[73] whisker_0.4.1 mime_0.12
[75] xml2_1.3.3 compiler_4.2.2
[77] rstudioapi_0.14 filelock_1.0.2
[79] curl_5.0.0 png_0.1-8
[81] interactiveDisplayBase_1.34.0 bslib_0.4.2
[83] stringi_1.7.12 highr_0.10
[85] ps_1.7.2 RSpectra_0.16-1
[87] Matrix_1.5-3 vctrs_0.5.2
[89] pillar_1.8.1 lifecycle_1.0.3
[91] BiocManager_1.30.20 jquerylib_0.1.4
[93] data.table_1.14.8 bitops_1.0-7
[95] corpcor_1.6.10 httpuv_1.6.9
[97] rtracklayer_1.56.1 latticeExtra_0.6-30
[99] R6_2.5.1 BiocIO_1.6.0
[101] promises_1.2.0.1 codetools_0.2-19
[103] SummarizedExperiment_1.26.1 rprojroot_2.0.3
[105] rjson_0.2.21 withr_2.5.0
[107] GenomicAlignments_1.32.1 Rsamtools_2.12.0
[109] GenomeInfoDbData_1.2.8 parallel_4.2.2
[111] hms_1.1.2 rpart_4.1.19
[113] grid_4.2.2 rmarkdown_2.20
[115] MatrixGenerics_1.8.1 git2r_0.31.0
[117] getPass_0.2-2 base64enc_0.1-3
[119] shiny_1.7.4 ellipse_0.4.3
[121] interp_1.1-3 restfulr_0.0.15