Source: https://github.com/markziemann/fran_mbd/blob/master/main_report_integration.Rmd
I will perform a multi-contrast pathway analysis involving RNA expression and DNA methylation data looking at differences caused by acetate and high fibre diet.
suppressPackageStartupMessages({
# to be run in R4
library("mitch")
})Importing the DESeq2 tables I generated earlier.
rna_heart_ctrl_vs_acetate <- read.table("heart_ctrl_vs_acetate_rna.tsv")
rna_heart_ctrl_vs_hifibre <- read.table("heart_ctrl_vs_hifibre_rna.tsv")
rna_spleen_ctrl_vs_acetate <- read.table("spleen_ctrl_vs_acetate_rna.tsv")
rna_spleen_ctrl_vs_hifibre <- read.table("spleen_ctrl_vs_hifibre_rna.tsv")
meth_heart_ctrl_vs_acetate <- read.table("heart_ctrl_vs_acetate_meth.tsv")
meth_heart_ctrl_vs_hifibre <- read.table("heart_ctrl_vs_hifibre_meth.tsv")
meth_spleen_ctrl_vs_acetate <- read.table("spleen_ctrl_vs_acetate_meth.tsv")
meth_spleen_ctrl_vs_hifibre <- read.table("spleen_ctrl_vs_hifibre_meth.tsv")
# strip the gene names out to make downstream analysis easier
rownames(rna_heart_ctrl_vs_acetate) <- sapply(strsplit(rownames(rna_heart_ctrl_vs_acetate),"_"),"[[",1)
rownames(rna_heart_ctrl_vs_hifibre) <- sapply(strsplit(rownames(rna_heart_ctrl_vs_hifibre),"_"),"[[",1)
rownames(rna_spleen_ctrl_vs_acetate) <- sapply(strsplit(rownames(rna_spleen_ctrl_vs_acetate),"_"),"[[",1)
rownames(rna_spleen_ctrl_vs_hifibre) <- sapply(strsplit(rownames(rna_spleen_ctrl_vs_hifibre),"_"),"[[",1)
rownames(meth_heart_ctrl_vs_acetate) <- sapply(strsplit(rownames(meth_heart_ctrl_vs_acetate),"_"),"[[",1)
rownames(meth_heart_ctrl_vs_hifibre) <- sapply(strsplit(rownames(meth_heart_ctrl_vs_hifibre),"_"),"[[",1)
rownames(meth_spleen_ctrl_vs_acetate) <- sapply(strsplit(rownames(meth_spleen_ctrl_vs_acetate),"_"),"[[",1)
rownames(meth_spleen_ctrl_vs_hifibre) <- sapply(strsplit(rownames(meth_spleen_ctrl_vs_hifibre),"_"),"[[",1)# gene sets
download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip",
destfile="ReactomePathways.gmt.zip")
unzip("ReactomePathways.gmt.zip",overwrite = TRUE)
genesets <- gmt_import("ReactomePathways.gmt")
# gene table
m2h <- read.table("mouse2human.txt.sort")
m2h[,1]=NULLx <- list("rna"=rna_heart_ctrl_vs_acetate,"meth"=meth_heart_ctrl_vs_acetate)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)## Note: Mean no. genes in input = 23118.5## Note: no. genes in output = 11707## Note: estimated proportion of input genes in output = 0.506capture.output(
res <- mitch_calc(m,genesets=genesets,priority="effect")
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set
## 315 Establishment of Sister Chromatid Cohesion
## 625 Mitotic Telophase/Cytokinesis
## 414 Glucuronidation
## 1215 Viral mRNA Translation
## 744 Peptide chain elongation
## 193 Constitutive Signaling by NOTCH1 HD Domain Mutants
## 1025 Signaling by NOTCH1 HD Domain Mutants in Cancer
## 976 Selenocysteine synthesis
## 271 Dissolution of Fibrin Clot
## 48 Activation of the pre-replicative complex
## 928 Response of EIF2AK4 (GCN2) to amino acid deficiency
## 320 Eukaryotic Translation Termination
## 203 Cyclin A/B1/B2 associated events during G2/M transition
## 225 DNA strand elongation
## 318 Eukaryotic Translation Elongation
## 455 Heme degradation
## 864 Recognition of DNA damage by PCNA-containing replication complex
## 617 Mitophagy
## 682 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
## 356 Formation of a pool of free 40S subunits
## setSize pMANOVA s.rna s.meth p.rna p.meth
## 315 10 4.253900e-04 0.71390955 0.11997948 9.251346e-05 5.113032e-01
## 625 10 5.543468e-04 0.68509874 0.20415491 1.757346e-04 2.637228e-01
## 414 11 4.900979e-04 0.56031588 0.40832919 1.292567e-03 1.904774e-02
## 1215 37 2.917320e-11 0.62740221 -0.18306584 3.972917e-11 5.415247e-02
## 744 37 1.121378e-10 0.61430325 -0.16367216 1.000118e-10 8.514360e-02
## 193 10 2.481157e-03 -0.46023767 0.41410618 1.174144e-02 2.337857e-02
## 1025 10 2.481157e-03 -0.46023767 0.41410618 1.174144e-02 2.337857e-02
## 976 40 1.803173e-10 0.56703951 -0.20611983 5.454957e-10 2.419159e-02
## 271 10 6.201525e-03 0.51999658 0.28390186 4.411800e-03 1.201261e-01
## 48 26 1.249212e-06 0.59065017 0.01361185 1.856571e-07 9.044275e-01
## 928 44 2.066483e-10 0.57795827 -0.04296805 3.283386e-11 6.222340e-01
## 320 40 2.362539e-09 0.55236565 -0.13956458 1.497944e-09 1.269719e-01
## 203 19 1.172866e-04 0.54433697 -0.12385172 4.002090e-05 3.501912e-01
## 225 26 9.024083e-06 0.54290004 -0.03642997 1.657264e-06 7.479454e-01
## 318 40 1.775977e-08 0.52542642 -0.12594926 8.958190e-09 1.684335e-01
## 455 10 1.066175e-02 0.29040780 -0.45484312 1.118651e-01 1.276432e-02
## 864 21 8.297836e-05 0.51523598 -0.16026503 4.371555e-05 2.037888e-01
## 617 19 3.223508e-04 -0.02049335 -0.53144476 8.771529e-01 6.071578e-05
## 682 41 3.762444e-08 0.51248364 -0.10457740 1.370317e-08 2.469880e-01
## 356 46 4.546524e-09 0.49743664 -0.15668729 5.356992e-09 6.621354e-02
## s.dist SD p.adjustMANOVA
## 315 0.7239212 0.4199720 6.295772e-03
## 625 0.7148703 0.3400786 7.611411e-03
## 414 0.6933157 0.1074708 7.086703e-03
## 1215 0.6535646 0.5730875 9.174972e-09
## 744 0.6357335 0.5501117 2.015277e-08
## 193 0.6191144 0.6182545 2.477219e-02
## 1025 0.6191144 0.6182545 2.477219e-02
## 976 0.6033400 0.5467062 2.835490e-08
## 271 0.5924498 0.1669442 5.307155e-02
## 48 0.5908070 0.4080277 4.910963e-05
## 928 0.5795533 0.4390612 2.888484e-08
## 320 0.5697246 0.4892686 2.122910e-07
## 203 0.5582490 0.4724808 2.202187e-03
## 225 0.5441209 0.4096482 2.588103e-04
## 318 0.5403111 0.4605922 1.117089e-06
## 455 0.5396471 0.5269720 7.797954e-02
## 864 0.5395859 0.4776513 1.683658e-03
## 617 0.5318397 0.3612972 5.133130e-03
## 682 0.5230448 0.4363280 1.972148e-06
## 356 0.5215306 0.4625355 3.574704e-07unlink("heart_ctrl_vs_acetate_integrate.html")
capture.output(
mitch_report(res,outfile=paste("heart_ctrl_vs_acetate_integrate.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpYKylDb/./heart_ctrl_vs_acetate_integrate.RData ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md##
## Output created: /tmp/RtmpYKylDb/mitch_report.htmlx <- list("rna"=rna_heart_ctrl_vs_hifibre,"meth"=meth_heart_ctrl_vs_hifibre)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)## Note: Mean no. genes in input = 23496## Note: no. genes in output = 11716## Note: estimated proportion of input genes in output = 0.499capture.output(
res <- mitch_calc(m,genesets=genesets,priority="effect")
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set
## 414 Glucuronidation
## 503 Interferon alpha/beta signaling
## 179 Classical antibody-mediated complement activation
## 486 Initial triggering of complement
## 751 Phosphorylation of CD3 and TCR zeta chains
## 542 LGI-ADAM interactions
## 661 Negative regulation of TCF-dependent signaling by WNT ligand antagonists
## 202 Creation of C4 and C2 activators
## 985 Signaling by Activin
## 912 Removal of the Flap Intermediate
## 717 PI-3K cascade:FGFR2
## 719 PI-3K cascade:FGFR4
## 166 Cholesterol biosynthesis
## 913 Removal of the Flap Intermediate from the C-strand
## 449 HSF1-dependent transactivation
## 788 Processive synthesis on the lagging strand
## 741 Peptide chain elongation
## 956 STING mediated induction of host immune responses
## 467 IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
## 1118 TRAF6-mediated induction of TAK1 complex within TLR4 complex
## setSize pMANOVA s.rna s.meth p.rna p.meth
## 414 11 2.858383e-05 0.5243835 0.60046600 2.602166e-03 0.0005641229
## 503 42 2.730068e-14 0.6487126 -0.27349136 3.434660e-13 0.0021787923
## 179 10 6.737190e-04 0.6836152 -0.13919358 1.815204e-04 0.4460616028
## 486 19 1.212503e-06 0.6137561 -0.31759380 3.628085e-06 0.0165808118
## 751 10 1.647562e-03 0.6374338 -0.14416539 4.822738e-04 0.4299860274
## 542 11 9.862501e-04 -0.5934604 -0.26107724 6.542865e-04 0.1338782267
## 661 10 2.053361e-03 -0.6328635 0.10954212 5.294930e-04 0.5487252619
## 202 12 1.552352e-03 0.5847573 -0.13170711 4.526898e-04 0.4296655493
## 985 10 5.057947e-03 -0.5267897 0.27314198 3.922616e-03 0.1348274406
## 912 11 3.118552e-03 0.4385771 -0.39613996 1.179151e-02 0.0229304925
## 717 14 8.001451e-04 -0.5112557 0.27909759 9.271195e-04 0.0706670181
## 719 11 3.921024e-03 -0.5106054 0.27351947 3.367297e-03 0.1163157862
## 166 20 4.460525e-05 -0.5386029 -0.21130301 3.052152e-05 0.1019930216
## 913 12 2.804901e-03 0.4805195 -0.30859820 3.953563e-03 0.0642302094
## 449 26 3.162169e-06 -0.5599263 -0.10909390 7.744726e-07 0.3358798943
## 788 12 3.089530e-03 0.4761050 -0.30674698 4.298819e-03 0.0658452517
## 741 37 2.921664e-08 0.5578157 0.04620675 4.322418e-09 0.6269674378
## 956 11 6.756873e-03 0.4333346 -0.33872083 1.283870e-02 0.0517943768
## 467 11 7.153838e-03 -0.3417498 0.42691934 4.973532e-02 0.0142315088
## 1118 11 7.153838e-03 -0.3417498 0.42691934 4.973532e-02 0.0142315088
## s.dist SD p.adjustMANOVA
## 414 0.7972061 0.05379844 8.756414e-04
## 503 0.7040068 0.65209670 3.428965e-11
## 179 0.6976422 0.58181369 1.191818e-02
## 486 0.6910589 0.65856384 9.518151e-05
## 751 0.6535331 0.55267408 2.200756e-02
## 542 0.6483492 0.23503042 1.638541e-02
## 661 0.6422738 0.52496004 2.578074e-02
## 202 0.5994063 0.50661688 2.142588e-02
## 985 0.5933919 0.56563710 4.410295e-02
## 912 0.5909964 0.59023412 3.291513e-02
## 717 0.5824756 0.55886418 1.376688e-02
## 719 0.5792502 0.55446003 3.903370e-02
## 166 0.5785690 0.23143600 1.273277e-03
## 913 0.5710795 0.55799046 3.076739e-02
## 449 0.5704550 0.31878665 1.497571e-04
## 788 0.5663654 0.55355997 3.288516e-02
## 741 0.5597262 0.36176217 5.242299e-06
## 956 0.5500097 0.54592565 5.304145e-02
## 467 0.5468575 0.54353119 5.512405e-02
## 1118 0.5468575 0.54353119 5.512405e-02unlink("heart_ctrl_vs_hifibre_integrate.html")
capture.output(
mitch_report(res,outfile=paste("heart_ctrl_vs_hifibre_integrate.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpYKylDb/./heart_ctrl_vs_hifibre_integrate.RData ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md##
## Output created: /tmp/RtmpYKylDb/mitch_report.htmlx <- list("rna"=rna_spleen_ctrl_vs_acetate,"meth"=meth_spleen_ctrl_vs_acetate)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)## Note: Mean no. genes in input = 19833.5## Note: no. genes in output = 10950## Note: estimated proportion of input genes in output = 0.552capture.output(
res <- mitch_calc(m,genesets=genesets,priority="effect")
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set setSize
## 542 Leading Strand Synthesis 12
## 754 Polymerase switching 12
## 220 DNA strand elongation 23
## 538 Lagging Strand Synthesis 16
## 481 Inhibition of replication initiation of damaged DNA by RB1/E2F1 12
## 598 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) 12
## 778 Processive synthesis on the lagging strand 12
## 902 Removal of the Flap Intermediate 11
## 390 GP1b-IX-V activation signalling 10
## 287 E2F mediated regulation of DNA replication 18
## 703 PCNA-Dependent Long Patch Base Excision Repair 15
## 1160 Translesion Synthesis by POLH 10
## 597 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) 12
## 452 Heme biosynthesis 11
## 1209 WNT5A-dependent internalization of FZD2, FZD5 and ROR2 12
## 596 Mismatch Repair 13
## 184 Condensation of Prophase Chromosomes 10
## 381 G1/S-Specific Transcription 23
## 484 Initiation of Nuclear Envelope (NE) Reformation 14
## 399 Gap-filling DNA repair synthesis and ligation in GG-NER 17
## pMANOVA s.rna s.meth p.rna p.meth s.dist
## 542 1.023463e-05 0.7945846 0.08110867 1.871533e-06 0.626731502 0.7987136
## 754 1.023463e-05 0.7945846 0.08110867 1.871533e-06 0.626731502 0.7987136
## 220 3.417504e-10 0.7922975 -0.06909490 4.699666e-11 0.566454359 0.7953046
## 538 6.646676e-07 0.7659022 0.07611579 1.125181e-07 0.598260670 0.7696752
## 481 3.245906e-05 0.6702551 0.35087920 5.811151e-05 0.035370264 0.7565435
## 598 4.042528e-05 0.7278448 0.17705857 1.264978e-05 0.288383120 0.7490713
## 778 4.889778e-05 0.7399738 0.06098007 9.042008e-06 0.714634281 0.7424822
## 902 1.210500e-04 0.7393978 -0.01608091 2.169936e-05 0.926443107 0.7395727
## 390 4.992354e-04 -0.7095064 0.06378428 1.022258e-04 0.726967372 0.7123677
## 287 1.499458e-06 0.5502348 0.43833089 5.320013e-05 0.001287253 0.7034858
## 703 2.466545e-05 0.6602835 0.18657522 9.521771e-06 0.211069880 0.6861375
## 1160 8.834401e-04 0.6343510 0.25533821 5.137997e-04 0.162170428 0.6838120
## 597 2.911563e-04 0.6505912 0.16838849 9.527545e-05 0.312646021 0.6720295
## 452 6.772728e-04 0.6146731 0.25168496 4.157868e-04 0.148458563 0.6642050
## 1209 3.694786e-04 0.5223380 0.40577193 1.732331e-03 0.014959899 0.6614287
## 596 3.059112e-04 0.6118469 0.19961176 1.336954e-04 0.212861041 0.6435848
## 184 2.071378e-03 0.4140585 0.48886654 2.339858e-02 0.007438631 0.6406520
## 381 7.671459e-07 0.6193394 0.15537500 2.722206e-07 0.197332998 0.6385317
## 484 1.908814e-04 0.5789529 0.26750444 1.765383e-04 0.083195380 0.6377657
## 399 4.616548e-05 0.6098482 0.13853902 1.341697e-05 0.322904225 0.6253862
## SD p.adjustMANOVA
## 542 0.50450369 9.801627e-05
## 754 0.50450369 9.801627e-05
## 220 0.60909641 1.519569e-08
## 538 0.48775267 8.443992e-06
## 481 0.22583285 2.767913e-04
## 598 0.38946469 3.289508e-04
## 778 0.48012107 3.757885e-04
## 902 0.53420413 8.514532e-04
## 390 0.54679908 2.864277e-03
## 287 0.07912800 1.761156e-05
## 703 0.33496233 2.241495e-04
## 1160 0.26800252 4.640856e-03
## 597 0.34096881 1.840049e-03
## 452 0.25667138 3.682116e-03
## 1209 0.08242468 2.243906e-03
## 596 0.29149424 1.913867e-03
## 184 0.05289728 1.011320e-02
## 381 0.32807238 9.647441e-06
## 484 0.22022729 1.291562e-03
## 399 0.33326593 3.637723e-04unlink("spleen_ctrl_vs_acetate_integrate.html")
capture.output(
mitch_report(res,outfile=paste("spleen_ctrl_vs_acetate_integrate.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpYKylDb/./spleen_ctrl_vs_acetate_integrate.RData ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md##
## Output created: /tmp/RtmpYKylDb/mitch_report.htmlx <- list("rna"=rna_spleen_ctrl_vs_hifibre,"meth"=meth_spleen_ctrl_vs_hifibre)
m <- mitch_import(x=x, DEtype="deseq2",geneTable=m2h)## Note: Mean no. genes in input = 19728.5## Note: no. genes in output = 10887## Note: estimated proportion of input genes in output = 0.552capture.output(
res <- mitch_calc(m,genesets=genesets,priority="effect")
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set setSize
## 171 Classical antibody-mediated complement activation 10
## 325 FCGR activation 15
## 194 Creation of C4 and C2 activators 14
## 480 Initial triggering of complement 20
## 251 Digestion 12
## 640 Na+/Cl- dependent neurotransmitter transporters 11
## 252 Digestion and absorption 13
## 158 Cholesterol biosynthesis 16
## 963 Signal regulatory protein family interactions 11
## 385 GABA synthesis, release, reuptake and degradation 11
## 863 Regulation of IFNA signaling 10
## 1207 eNOS activation 10
## 935 SRP-dependent cotranslational protein targeting to membrane 42
## 859 Regulation of Complement cascade 30
## 166 Citric acid cycle (TCA cycle) 13
## 578 Metabolism of nitric oxide: NOS3 activation and regulation 14
## 914 Retrograde neurotrophin signalling 12
## 432 HDMs demethylate histones 15
## 440 HIV elongation arrest and recovery 15
## 727 Pausing and recovery of HIV elongation 15
## pMANOVA s.rna s.meth p.rna p.meth s.dist
## 171 1.440546e-06 0.8636021 -0.37528730 2.246779e-06 0.039922271 0.9416205
## 325 3.167540e-05 0.6258339 -0.25336645 2.710190e-05 0.089436059 0.6751760
## 194 7.724307e-05 0.6427586 -0.18533458 3.126481e-05 0.230048196 0.6689451
## 480 2.624851e-06 0.6376001 -0.13938529 7.954289e-07 0.280772030 0.6526577
## 251 5.736317e-04 -0.6355862 0.09504981 1.377077e-04 0.568729738 0.6426541
## 640 1.371495e-03 -0.6170049 0.12879067 3.952322e-04 0.459666224 0.6303032
## 252 7.454799e-04 -0.5925638 0.12693652 2.163763e-04 0.428264281 0.6060072
## 158 3.557312e-04 -0.5748551 -0.03639270 6.869038e-05 0.801101283 0.5760059
## 963 3.987849e-03 0.4274549 -0.38382260 1.411361e-02 0.027540414 0.5744889
## 385 7.316149e-03 -0.5431475 0.04904878 1.815232e-03 0.778258218 0.5453577
## 863 1.310116e-02 0.4554840 0.29281052 1.264148e-02 0.108942807 0.5414829
## 1207 1.202383e-02 0.1608900 -0.51622690 3.784584e-01 0.004707644 0.5407178
## 935 2.000991e-08 0.5166831 0.13079980 6.940745e-09 0.142840913 0.5329822
## 859 2.801145e-06 0.4901354 -0.20331583 3.397638e-06 0.054091018 0.5306317
## 166 4.287069e-03 -0.5187391 -0.11165660 1.203717e-03 0.485923865 0.5306199
## 578 2.608992e-03 0.1694630 -0.50220073 2.724474e-01 0.001142110 0.5300220
## 914 6.512644e-03 0.2135785 -0.48076628 2.003110e-01 0.003936237 0.5260723
## 432 2.192129e-03 -0.5208364 0.02609762 4.793356e-04 0.861136559 0.5214898
## 440 3.507006e-03 -0.3737062 -0.34009075 1.223673e-02 0.022617397 0.5052900
## 727 3.507006e-03 -0.3737062 -0.34009075 1.223673e-02 0.022617397 0.5052900
## SD p.adjustMANOVA
## 171 0.87602710 1.110121e-04
## 325 0.62168856 1.346751e-03
## 194 0.58555030 2.506334e-03
## 480 0.54941162 1.804304e-04
## 251 0.51663768 1.040129e-02
## 640 0.52735711 1.951850e-02
## 252 0.50876353 1.259146e-02
## 158 0.38075043 7.582375e-03
## 963 0.57365985 3.841420e-02
## 385 0.41874604 5.895955e-02
## 863 0.11502756 8.731748e-02
## 1207 0.47879392 8.236321e-02
## 935 0.27286072 2.242929e-06
## 859 0.49034407 1.817796e-04
## 166 0.28785081 4.004512e-02
## 578 0.47493800 3.153811e-02
## 914 0.49097594 5.375903e-02
## 432 0.38674075 2.786490e-02
## 440 0.02376968 3.487208e-02
## 727 0.02376968 3.487208e-02unlink("spleen_ctrl_vs_hifibre_integrate.html")
capture.output(
mitch_report(res,outfile=paste("spleen_ctrl_vs_hifibre_integrate.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmpYKylDb/./spleen_ctrl_vs_hifibre_integrate.RData ".##
##
## processing file: mitch.Rmd## output file: /mnt/bfx6/bfx/francine/fran_methylome/redo2020/mitch.knit.md##
## Output created: /tmp/RtmpYKylDb/mitch_report.htmlEnd of report
sessionInfo()## R version 4.0.2 (2020-06-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] pkgload_1.1.0 GGally_2.0.0 ggplot2_3.3.2 reshape2_1.4.4
## [5] beeswarm_0.2.3 gplots_3.0.3 gtools_3.8.2 tibble_3.0.1
## [9] dplyr_1.0.0 echarts4r_0.3.2 mitch_1.0.6
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.4.6 assertthat_0.2.1 rprojroot_1.3-2 digest_0.6.25
## [5] mime_0.9 R6_2.4.1 plyr_1.8.6 backports_1.1.8
## [9] evaluate_0.14 highr_0.8 pillar_1.4.4 rlang_0.4.6
## [13] gdata_2.18.0 rmarkdown_2.3 desc_1.2.0 labeling_0.3
## [17] stringr_1.4.0 htmlwidgets_1.5.1 munsell_0.5.0 shiny_1.5.0
## [21] compiler_4.0.2 httpuv_1.5.4 xfun_0.15 pkgconfig_2.0.3
## [25] htmltools_0.5.0 tidyselect_1.1.0 gridExtra_2.3 reshape_0.8.8
## [29] crayon_1.3.4 withr_2.2.0 later_1.1.0.1 MASS_7.3-51.6
## [33] bitops_1.0-6 grid_4.0.2 jsonlite_1.7.0 xtable_1.8-4
## [37] gtable_0.3.0 lifecycle_0.2.0 magrittr_1.5 scales_1.1.1
## [41] KernSmooth_2.23-17 stringi_1.4.6 farver_2.0.3 promises_1.1.1
## [45] testthat_2.3.2 ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.1
## [49] pbmcapply_1.5.0 RColorBrewer_1.1-2 tools_4.0.2 glue_1.4.1
## [53] purrr_0.3.4 parallel_4.0.2 fastmap_1.0.1 yaml_2.2.1
## [57] colorspace_1.4-1 caTools_1.18.0 knitr_1.29