Run_all_analysis
ERM
20230410
Last updated: 2023-04-10
Checks: 7 0
Knit directory: Cardiotoxicity/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 8ca4c7e | reneeisnowhere | 2023-04-10 | first rmd commit |
| Rmd | 2e69969 | reneeisnowhere | 2023-04-10 | adding data |
| Rmd | 0f1f1da | reneeisnowhere | 2023-04-10 | final run analysis |
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 PC7 PC8 PC9
Da.1.3h 44.793907 -4.229684 25.33474 -35.96203 5.114646 -24.124808 31.452389
Do.1.3h 24.565270 -8.522490 -19.86738 -19.00810 7.401478 -10.801889 14.365242
Ep.1.3h 33.103318 -9.146883 18.17321 -43.12911 4.369781 -33.782214 14.797673
Mi.1.3h 19.048074 -14.540036 -9.00047 -24.33769 1.439095 -13.595652 11.576765
Tr.1.3h 2.646249 -17.004856 -34.18428 -11.83222 -3.927467 -7.786517 9.362868
Ve.1.3h 12.636907 -4.140009 -39.84065 -17.16481 -1.117439 1.089213 2.212854
PC10 PC11 PC12 PC13 PC14 PC15
Da.1.3h -4.133988 10.266518 -11.62439 12.884620 14.529370 -2.9650236
Do.1.3h -9.677611 -10.846911 -18.72890 8.077905 -8.055543 0.6439353
Ep.1.3h 13.493488 10.505317 -22.23871 20.348212 -1.317876 -10.3964742
Mi.1.3h -5.333702 3.850642 -14.44780 16.059986 -10.963660 -4.5555149
Tr.1.3h -2.272615 1.757867 -12.04874 28.065514 -8.830059 -0.3950799
Ve.1.3h -11.697015 -14.875556 -10.42955 21.460187 -17.059644 3.0823271
PC16 PC17 PC18 PC19 PC20 PC21 PC22
Da.1.3h 14.526291 -4.071934 14.935593 -8.019220 5.083468 -2.891750 7.4922608
Do.1.3h 13.799184 8.746834 4.416582 2.323326 -0.237433 4.027698 1.0664447
Ep.1.3h 6.963875 -2.522538 6.259495 1.329862 7.445919 4.390526 -4.1356648
Mi.1.3h 7.016836 8.396316 -6.573762 6.180844 10.158825 -4.026253 8.5762521
Tr.1.3h -1.569298 5.561989 -2.813333 3.011656 -8.311216 3.854712 -0.2389895
Ve.1.3h 11.559969 12.418994 3.277303 3.045864 -1.331373 1.180896 8.1040510
PC23 PC24 PC25 PC26 PC27 PC28
Da.1.3h -12.222479 6.748697 -5.5187510 8.74956626 -5.361678 3.3209763
Do.1.3h 3.816818 5.130011 1.4608624 -2.05098419 -4.470525 -4.3785841
Ep.1.3h 1.342287 -1.025011 1.1961204 -1.83068384 -5.262485 -3.6490931
Mi.1.3h 6.296190 -8.170311 -4.2786507 1.44302957 -6.815788 -0.1255762
Tr.1.3h 0.480255 1.895733 -1.8505180 -3.42444400 3.818558 1.1025238
Ve.1.3h 2.329309 11.619652 0.1657874 -0.01026589 0.969233 1.5911490
PC29 PC30 PC31 PC32 PC33 PC34
Da.1.3h 3.1706172 10.0506445 -4.458641 -10.0657089 -4.568317 13.6896144
Do.1.3h 6.3590470 -0.4283709 -2.555236 4.1919429 1.905148 -0.1752443
Ep.1.3h -0.5356397 1.4180942 -2.663608 -0.2148416 6.325774 -1.7110775
Mi.1.3h 1.3055415 -1.6910496 -3.946695 -0.8189906 3.051660 -2.1705031
Tr.1.3h -10.1920623 -10.7690648 3.601393 -1.6219667 -2.148793 -6.5626415
Ve.1.3h 6.1910931 -8.9587536 2.605718 -0.8448476 -2.629549 -8.5472192
PC35 PC36 PC37 PC38 PC39 PC40
Da.1.3h 7.2770521 3.2792454 -10.4894361 -4.30733107 -5.849739 -2.687516
Do.1.3h -0.9260830 1.7794615 2.8937075 0.89458004 5.157193 -1.280842
Ep.1.3h -0.1554011 1.8404528 -0.5143910 0.09648441 7.440072 1.408057
Mi.1.3h -5.3032004 4.8268423 -0.8944211 -0.20732412 1.388244 2.270157
Tr.1.3h -3.9454575 -6.2932182 6.6367557 -4.50448821 -3.378639 -1.416561
Ve.1.3h -3.7739170 -0.1062269 6.0369386 0.06051097 2.279350 -4.526761
PC41 PC42 PC43 PC44 PC45 PC46
Da.1.3h -1.262007 -1.035504 8.2056950 3.8989026 6.24638692 3.4089655
Do.1.3h -0.186425 3.146487 2.9289474 -2.7419697 0.16004844 -7.3339956
Ep.1.3h 4.785448 2.860477 -3.1017019 1.3166174 -0.84506266 -0.4454939
Mi.1.3h 10.942509 2.936674 -0.1040299 -0.5854175 -6.08082071 -2.3049328
Tr.1.3h -6.486757 3.121272 -1.3534505 6.1969829 4.03540141 5.6064581
Ve.1.3h -4.489930 -3.442894 0.8969077 -6.3163924 -0.01184596 4.6677253
PC47 PC48 PC49 PC50 PC51 PC52
Da.1.3h 1.7245768 -1.8463393 -3.2997189 -2.553965 -4.419379561 -0.9948072
Do.1.3h -0.7494901 -1.4034252 -1.3011594 2.148875 1.813487415 4.3374340
Ep.1.3h 0.3053048 3.4956568 3.7115134 -1.482656 1.956967253 0.7068073
Mi.1.3h 1.2445851 -0.3253066 0.1115562 1.112562 -0.005470513 1.2400374
Tr.1.3h 6.9667641 -5.7857939 6.0033788 -1.871588 -6.585480377 -9.1835137
Ve.1.3h -10.0164441 4.2872411 -3.7138782 2.309897 6.500352335 1.5133235
PC53 PC54 PC55 PC56 PC57 PC58
Da.1.3h -5.461271 -4.2780958 2.7732012 1.1512850 0.05958554 0.5085057
Do.1.3h 11.532018 3.0961716 0.2045428 2.7726775 -7.78100383 9.8903571
Ep.1.3h 3.930239 2.9214130 -2.5147902 1.5920310 -6.83905904 0.4921512
Mi.1.3h -1.225530 6.0946473 -3.2895157 -2.3905055 11.01150136 -8.2144469
Tr.1.3h 6.871187 -9.5578828 -1.7000342 6.7087662 3.83241538 -1.7379386
Ve.1.3h -12.999179 -0.9773753 6.9444669 -0.5177584 1.08538726 -3.6088769
PC59 PC60 PC61 PC62 PC63 PC64
Da.1.3h 0.6947479 0.2495424 0.9451556 0.8788365 1.3554167 0.6912746
Do.1.3h 7.8141494 3.6710031 0.9438323 0.9012747 -4.4136351 -7.0408006
Ep.1.3h -5.7893006 1.6745696 -1.1681311 -2.5273166 2.8633028 -1.5009335
Mi.1.3h -1.6489538 -6.7904105 -10.5875997 3.6093798 -1.3148648 3.9122749
Tr.1.3h 1.4601813 0.7305937 -0.1613648 -0.1971653 -1.4000034 1.4957112
Ve.1.3h 0.9947420 0.6377554 7.8729369 -0.1632842 0.9153045 0.9037070
PC65 PC66 PC67 PC68 PC69 PC70
Da.1.3h 0.09636128 -2.1975401 -1.3284695 -0.04825934 -1.080057 0.7908676
Do.1.3h 1.28715194 -7.0105439 -2.4649046 0.86945034 -6.246263 1.5887178
Ep.1.3h -3.99683169 10.2834224 5.1907167 0.96314910 11.571833 -1.6664249
Mi.1.3h 3.45191027 -3.1257619 -2.1146401 -1.55735609 -4.500124 0.1069785
Tr.1.3h -0.77700790 1.4183639 -0.1288110 -2.85040677 -1.181816 1.4809394
Ve.1.3h 2.61255032 0.1308984 0.7723808 0.77368136 3.262802 -0.9221706
PC71 PC72
Da.1.3h -0.3614398 -6.675299e-14
Do.1.3h -0.9465562 -1.265367e-13
Ep.1.3h 2.4218610 -5.043584e-14
Mi.1.3h -0.1963754 -1.127307e-13
Tr.1.3h -1.2175642 -8.186241e-14
Ve.1.3h -0.8285151 -5.746066e-14
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 DBI_1.1.3
[35] Rcpp_1.0.10 htmlTable_2.4.1
[37] xtable_1.8-4 progress_1.2.2
[39] foreign_0.8-84 bit_4.0.5
[41] htmlwidgets_1.6.1 httr_1.4.5
[43] ellipsis_0.3.2 farver_2.1.1
[45] pkgconfig_2.0.3 XML_3.99-0.13
[47] nnet_7.3-18 deldir_1.0-6
[49] sass_0.4.5 locfit_1.5-9.7
[51] utf8_1.2.3 labeling_0.4.2
[53] tidyselect_1.2.0 rlang_1.0.6
[55] later_1.3.0 munsell_0.5.0
[57] BiocVersion_3.15.2 tools_4.2.2
[59] cachem_1.0.7 cli_3.6.0
[61] generics_0.1.3 RSQLite_2.3.0
[63] evaluate_0.20 fastmap_1.1.1
[65] yaml_2.3.7 processx_3.8.0
[67] knitr_1.42 bit64_4.0.5
[69] fs_1.6.1 KEGGREST_1.36.3
[71] RBGL_1.72.0 whisker_0.4.1
[73] mime_0.12 xml2_1.3.3
[75] compiler_4.2.2 rstudioapi_0.14
[77] filelock_1.0.2 curl_5.0.0
[79] png_0.1-8 interactiveDisplayBase_1.34.0
[81] bslib_0.4.2 stringi_1.7.12
[83] highr_0.10 ps_1.7.2
[85] RSpectra_0.16-1 Matrix_1.5-3
[87] vctrs_0.5.2 pillar_1.8.1
[89] lifecycle_1.0.3 BiocManager_1.30.20
[91] jquerylib_0.1.4 data.table_1.14.8
[93] bitops_1.0-7 corpcor_1.6.10
[95] httpuv_1.6.9 rtracklayer_1.56.1
[97] latticeExtra_0.6-30 R6_2.5.1
[99] BiocIO_1.6.0 promises_1.2.0.1
[101] codetools_0.2-19 SummarizedExperiment_1.26.1
[103] rprojroot_2.0.3 rjson_0.2.21
[105] withr_2.5.0 GenomicAlignments_1.32.1
[107] Rsamtools_2.12.0 GenomeInfoDbData_1.2.8
[109] parallel_4.2.2 hms_1.1.2
[111] rpart_4.1.19 grid_4.2.2
[113] rmarkdown_2.20 MatrixGenerics_1.8.1
[115] git2r_0.31.0 getPass_0.2-2
[117] base64enc_0.1-3 shiny_1.7.4
[119] ellipse_0.4.3 interp_1.1-3
[121] restfulr_0.0.15