Last updated: 2018-12-04

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    Rmd 8311225 Jason Willwerscheid 2018-12-04 workflowr::wflow_publish(“analysis/pulseseq.Rmd”)

Introduction and Code

I fit 30 factors with normal-mixture priors to the PulseSeq dataset discussed in Montoro et al. I removed all genes with zero total counts and did a log1p transform of the counts. I used the following calls.

# Add 30 factors with rough backfits after every 5 factors.
fl <- flashier(data, greedy.Kmax = 30, var.type = 1, prior.type = "normal.mix", ash.param = list(optmethod = "mixSQP"), backfit.every = 5, final.backfit = TRUE, backfit.order = "montaigne", warmstart.backfits = FALSE)
# Process time on RCC cluster: 92 minutes

# Do a more thorough backfit.
fl <- flashier(data, flash.init = fl, greedy.Kmax = 0, var.type = 1, prior.type = "normal.mix", ash.param = list(optmethod = "mixSQP"), final.backfit = TRUE, backfit.order = "dropout", warmstart.backfits = FALSE, backfit.maxiter = 500)
# Process time: 266 minutes

The following code is used to produce the boxplots and tables below.

suppressMessages({
  library(ggplot2)
  library(topGO)
  library(org.Mm.eg.db)
})
#> Warning: package 'ggplot2' was built under R version 3.4.4

fl <- readRDS("~/Downloads/PulseSeq30_backfit.rds")
# Remove large data object to free up memory.
fl$fit$Y <- NULL

# Data frame containing cell type and loadings for each factor.
PSdf <- data.frame(fl$loadings$normalized.loadings[[2]])
cell.names <- rownames(fl$loadings$normalized.loadings[[2]])
cell.types <- as.factor(sapply(strsplit(cell.names, "_"), `[`, 5))
levels(cell.types) <- c("Bas", "Cil", "Clb", "Hil", "Gb1", "Gb2", "GbP",
                        "Ion", "Nec", "Prl", "Tf1", "Tf2", "TfP")
PSdf$cell.type <- cell.types

# Need to select signficant genes for topGO.
#   Scale gene loadings by scale constant * maximum cell loading.
s <- fl$loadings$scale.constant * 
  apply(abs(fl$loadings$normalized.loadings[[2]]), 2, max)
gene.loadings <- fl$loadings$normalized.loadings[[1]]
gene.loadings <- gene.loadings * rep(s, each = nrow(gene.loadings))
#   Get a pseudo-t statistic by dividing by the residual SE.
gene.t <- gene.loadings * sqrt(fl$fit$tau)
#   Convert to a p-value.
gene.p <- 2 * (1 - pnorm(abs(gene.t)))
#   Select significant genes using Benjamini-Hochberg.
BH <- function(k, alpha = 0.01) {
  pvals <- gene.p[, k]
  selected <- rep(0, length(pvals))
  names(selected) <- names(pvals)
  
  n <- length(pvals)
  sorted.pvals <- sort(pvals)
  BH <- sorted.pvals < alpha / (n - 0:(n - 1))
  cutoff <- min(which(!BH))
  selected[pvals < sorted.pvals[cutoff]] <- 1
  
  return(selected)
}
gene.sig <- sapply(1:ncol(gene.p), BH)

# How many significant genes per factor are there?
colSums(gene.sig)
#>  [1]  319  565   42   79  192    2  171  194   36 1495    1 1946    0   72
#> [15]   11   54    0   84    0  246  135    0  210   19    0  112  180  159
#> [29]  188  929

# I will only look at the factors with at least ten significant genes.
kset <- (1:ncol(gene.p))[colSums(gene.sig) > 9]

# Set up topGOdata object.
GO.list <- as.factor(gene.sig[, 1])
GOdata <- new("topGOdata", ontology = "BP", allGenes = GO.list,
              annot = annFUN.org, mapping = "org.Mm.eg", ID = "symbol")
#> 
#> Building most specific GOs .....
#>  ( 11574 GO terms found. )
#> 
#> Build GO DAG topology ..........
#>  ( 15465 GO terms and 36320 relations. )
#> 
#> Annotating nodes ...............
#>  ( 17307 genes annotated to the GO terms. )
# Loop over kset.
for (k in kset) {
  cat(paste("## Factor", k, "\n"))
  fctr <- paste0("X", k)
  plot(ggplot(PSdf, aes_string(x = "cell.type", y = fctr)) +
         geom_boxplot(outlier.shape = NA, color = "red") +
         geom_jitter(position = position_jitter(0.2), cex = 0.1) +
         labs(x = "Cell Type", y = paste("Factor", k, "value")))
  GOdata@allScores <- as.factor(gene.sig[, k])
  result <- suppressMessages(
    runTest(GOdata, algorithm = "classic", statistic = "fisher")
  )
  allRes <- GenTable(GOdata, classic = result, topNodes = 10)
  print(knitr::kable(allRes))
  cat("\n")
}

Factor 1

GO.ID Term Annotated Significant Expected classic
GO:0006412 translation 554 84 9.51 < 1e-30
GO:0043043 peptide biosynthetic process 575 84 9.87 < 1e-30
GO:0006518 peptide metabolic process 700 90 12.01 < 1e-30
GO:0043604 amide biosynthetic process 644 85 11.05 < 1e-30
GO:0043603 cellular amide metabolic process 830 91 14.24 < 1e-30
GO:1901566 organonitrogen compound biosynthetic pro… 1460 106 25.05 < 1e-30
GO:0034641 cellular nitrogen compound metabolic pro… 5337 177 91.59 5.7e-25
GO:0044271 cellular nitrogen compound biosynthetic … 3940 148 67.61 8.2e-25
GO:0044249 cellular biosynthetic process 4799 162 82.35 1.0e-22
GO:1901576 organic substance biosynthetic process 4895 163 84.00 3.1e-22

Factor 2

GO.ID Term Annotated Significant Expected classic
GO:0044782 cilium organization 291 89 8.61 <1e-30
GO:0060271 cilium assembly 272 82 8.05 <1e-30
GO:0003341 cilium movement 69 45 2.04 <1e-30
GO:0007018 microtubule-based movement 242 70 7.16 <1e-30
GO:0070925 organelle assembly 672 104 19.88 <1e-30
GO:0030031 cell projection assembly 450 85 13.31 <1e-30
GO:0120031 plasma membrane bounded cell projection … 443 84 13.11 <1e-30
GO:0007017 microtubule-based process 639 99 18.90 <1e-30
GO:0035082 axoneme assembly 60 37 1.78 <1e-30
GO:0001578 microtubule bundle formation 88 39 2.60 <1e-30

Factor 3

GO.ID Term Annotated Significant Expected classic
GO:0006412 translation 554 17 1.31 2.3e-15
GO:0043043 peptide biosynthetic process 575 17 1.36 4.2e-15
GO:0043604 amide biosynthetic process 644 17 1.53 2.7e-14
GO:0006518 peptide metabolic process 700 17 1.66 1.0e-13
GO:0043603 cellular amide metabolic process 830 17 1.97 1.6e-12
GO:0042274 ribosomal small subunit biogenesis 68 7 0.16 2.1e-10
GO:0022613 ribonucleoprotein complex biogenesis 379 11 0.90 8.4e-10
GO:0019730 antimicrobial humoral response 51 6 0.12 2.0e-09
GO:0042254 ribosome biogenesis 251 9 0.59 5.7e-09
GO:1901566 organonitrogen compound biosynthetic pro… 1460 17 3.46 1.1e-08

Factor 4

GO.ID Term Annotated Significant Expected classic
GO:0006412 translation 554 36 2.24 < 1e-30
GO:0043043 peptide biosynthetic process 575 36 2.33 < 1e-30
GO:0006518 peptide metabolic process 700 37 2.83 < 1e-30
GO:0043604 amide biosynthetic process 644 36 2.60 < 1e-30
GO:0043603 cellular amide metabolic process 830 37 3.36 1.6e-30
GO:1901566 organonitrogen compound biosynthetic pro… 1460 37 5.91 7.7e-22
GO:0009059 macromolecule biosynthetic process 4091 49 16.55 2.6e-16
GO:0044271 cellular nitrogen compound biosynthetic … 3940 48 15.94 4.0e-16
GO:0034645 cellular macromolecule biosynthetic proc… 3989 48 16.13 6.7e-16
GO:0010467 gene expression 4479 50 18.12 1.8e-15

Factor 5

GO.ID Term Annotated Significant Expected classic
GO:0006518 peptide metabolic process 700 27 6.92 1.2e-09
GO:0043603 cellular amide metabolic process 830 29 8.20 2.7e-09
GO:0043604 amide biosynthetic process 644 22 6.36 4.0e-07
GO:0006412 translation 554 20 5.47 6.0e-07
GO:0043043 peptide biosynthetic process 575 20 5.68 1.1e-06
GO:0050896 response to stimulus 6576 94 64.97 4.5e-06
GO:0050909 sensory perception of taste 51 6 0.50 1.1e-05
GO:0007186 G-protein coupled receptor signaling pat… 685 20 6.77 1.5e-05
GO:0006575 cellular modified amino acid metabolic p… 146 9 1.44 1.5e-05
GO:0050900 leukocyte migration 276 12 2.73 2.0e-05

Factor 7

GO.ID Term Annotated Significant Expected classic
GO:0007610 behavior 617 25 5.70 4.8e-10
GO:0099504 synaptic vesicle cycle 119 11 1.10 1.3e-08
GO:0048489 synaptic vesicle transport 127 11 1.17 2.6e-08
GO:0097480 establishment of synaptic vesicle locali… 127 11 1.17 2.6e-08
GO:0099003 vesicle-mediated transport in synapse 128 11 1.18 2.9e-08
GO:0097479 synaptic vesicle localization 134 11 1.24 4.6e-08
GO:0003008 system process 1429 35 13.21 7.5e-08
GO:0033555 multicellular organismal response to str… 84 9 0.78 8.0e-08
GO:0006887 exocytosis 295 15 2.73 1.0e-07
GO:0050877 nervous system process 867 26 8.02 1.0e-07

Factor 8

GO.ID Term Annotated Significant Expected classic
GO:0007049 cell cycle 1476 110 15.27 <1e-30
GO:0051301 cell division 526 75 5.44 <1e-30
GO:0022402 cell cycle process 947 89 9.79 <1e-30
GO:0000278 mitotic cell cycle 733 79 7.58 <1e-30
GO:1903047 mitotic cell cycle process 567 71 5.86 <1e-30
GO:0007059 chromosome segregation 285 56 2.95 <1e-30
GO:0000280 nuclear division 362 49 3.74 <1e-30
GO:0098813 nuclear chromosome segregation 222 40 2.30 <1e-30
GO:0048285 organelle fission 410 49 4.24 <1e-30
GO:0140014 mitotic nuclear division 231 40 2.39 <1e-30

Factor 9

GO.ID Term Annotated Significant Expected classic
GO:0009059 macromolecule biosynthetic process 4091 21 6.62 1.3e-08
GO:0034645 cellular macromolecule biosynthetic proc… 3989 20 6.45 7.5e-08
GO:0035914 skeletal muscle cell differentiation 69 5 0.11 8.0e-08
GO:0006412 translation 554 9 0.90 1.3e-07
GO:0071310 cellular response to organic substance 1800 14 2.91 1.6e-07
GO:0043043 peptide biosynthetic process 575 9 0.93 1.8e-07
GO:0031324 negative regulation of cellular metaboli… 2194 15 3.55 2.5e-07
GO:0044249 cellular biosynthetic process 4799 21 7.76 2.7e-07
GO:0070887 cellular response to chemical stimulus 2239 15 3.62 3.2e-07
GO:1901576 organic substance biosynthetic process 4895 21 7.92 3.9e-07

Factor 10

GO.ID Term Annotated Significant Expected classic
GO:0048519 negative regulation of biological proces… 4491 520 356.02 2.3e-24
GO:0048523 negative regulation of cellular process 4081 481 323.52 8.8e-24
GO:0006950 response to stress 2940 372 233.07 6.2e-23
GO:0006518 peptide metabolic process 700 133 55.49 5.6e-22
GO:0008219 cell death 1897 265 150.38 1.1e-21
GO:1901564 organonitrogen compound metabolic proces… 5378 581 426.34 2.9e-20
GO:0043603 cellular amide metabolic process 830 143 65.80 1.8e-19
GO:0048518 positive regulation of biological proces… 5006 542 396.85 1.2e-18
GO:0043043 peptide biosynthetic process 575 110 45.58 1.5e-18
GO:0006412 translation 554 107 43.92 2.3e-18

Factor 12

GO.ID Term Annotated Significant Expected classic
GO:0010941 regulation of cell death 1553 256 156.40 1.4e-16
GO:0048523 negative regulation of cellular process 4081 549 411.00 9.5e-16
GO:0048519 negative regulation of biological proces… 4491 592 452.29 2.6e-15
GO:0042981 regulation of apoptotic process 1401 232 141.10 2.9e-15
GO:0043067 regulation of programmed cell death 1418 234 142.81 3.2e-15
GO:0008219 cell death 1897 293 191.05 4.6e-15
GO:0043066 negative regulation of apoptotic process 823 155 82.88 4.7e-15
GO:0043069 negative regulation of programmed cell d… 839 157 84.50 5.5e-15
GO:0060548 negative regulation of cell death 932 168 93.86 1.9e-14
GO:0012501 programmed cell death 1752 272 176.45 3.0e-14

Factor 14

GO.ID Term Annotated Significant Expected classic
GO:0055067 monovalent inorganic cation homeostasis 137 7 0.49 5.7e-07
GO:0050801 ion homeostasis 673 13 2.41 5.9e-07
GO:0048878 chemical homeostasis 961 14 3.44 5.7e-06
GO:0055080 cation homeostasis 604 11 2.16 8.6e-06
GO:0098771 inorganic ion homeostasis 620 11 2.22 1.1e-05
GO:0006821 chloride transport 89 5 0.32 1.6e-05
GO:0030004 cellular monovalent inorganic cation hom… 97 5 0.35 2.5e-05
GO:0007588 excretion 50 4 0.18 3.0e-05
GO:0065008 regulation of biological quality 3110 25 11.14 3.1e-05
GO:0046068 cGMP metabolic process 55 4 0.20 4.4e-05

Factor 15

GO.ID Term Annotated Significant Expected classic
GO:0018979 trichloroethylene metabolic process 1 1 0.00 0.00012
GO:0018931 naphthalene metabolic process 2 1 0.00 0.00023
GO:0042196 chlorinated hydrocarbon metabolic proces… 2 1 0.00 0.00023
GO:0042197 halogenated hydrocarbon metabolic proces… 2 1 0.00 0.00023
GO:0090420 naphthalene-containing compound metaboli… 2 1 0.00 0.00023
GO:0019373 epoxygenase P450 pathway 20 1 0.00 0.00231
GO:0006805 xenobiotic metabolic process 43 1 0.00 0.00496
GO:0019369 arachidonic acid metabolic process 43 1 0.00 0.00496
GO:0071466 cellular response to xenobiotic stimulus 47 1 0.01 0.00542
GO:0009410 response to xenobiotic stimulus 53 1 0.01 0.00612

Factor 16

GO.ID Term Annotated Significant Expected classic
GO:0007049 cell cycle 1476 36 4.18 1.9e-28
GO:1903047 mitotic cell cycle process 567 23 1.61 1.2e-21
GO:0000278 mitotic cell cycle 733 24 2.08 1.8e-20
GO:0022402 cell cycle process 947 24 2.68 6.7e-18
GO:0051301 cell division 526 19 1.49 8.7e-17
GO:0006260 DNA replication 243 15 0.69 1.1e-16
GO:0006261 DNA-dependent DNA replication 120 12 0.34 5.2e-16
GO:0006259 DNA metabolic process 820 21 2.32 1.3e-15
GO:0006270 DNA replication initiation 30 8 0.08 1.3e-14
GO:0051276 chromosome organization 990 21 2.80 5.5e-14

Factor 18

GO.ID Term Annotated Significant Expected classic
GO:0001580 detection of chemical stimulus involved … 29 8 0.13 3.8e-13
GO:0050913 sensory perception of bitter taste 32 8 0.14 9.1e-13
GO:0050909 sensory perception of taste 51 9 0.22 9.8e-13
GO:0050912 detection of chemical stimulus involved … 33 8 0.14 1.2e-12
GO:0050907 detection of chemical stimulus involved … 45 8 0.20 1.8e-11
GO:0050906 detection of stimulus involved in sensor… 105 9 0.46 8.0e-10
GO:0009593 detection of chemical stimulus 71 8 0.31 8.1e-10
GO:0007606 sensory perception of chemical stimulus 141 9 0.62 1.1e-08
GO:0007600 sensory perception 511 14 2.24 4.1e-08
GO:0051606 detection of stimulus 193 9 0.85 1.7e-07

Factor 20

GO.ID Term Annotated Significant Expected classic
GO:0071594 thymocyte aggregation 2 2 0.02 0.00010
GO:0072535 tumor necrosis factor (ligand) superfami… 2 2 0.02 0.00010
GO:2000307 regulation of tumor necrosis factor (lig… 2 2 0.02 0.00010
GO:2000309 positive regulation of tumor necrosis fa… 2 2 0.02 0.00010
GO:0007099 centriole replication 27 4 0.27 0.00015
GO:0098534 centriole assembly 28 4 0.28 0.00017
GO:0001807 regulation of type IV hypersensitivity 3 2 0.03 0.00030
GO:0070489 T cell aggregation 3 2 0.03 0.00030
GO:0051298 centrosome duplication 61 5 0.62 0.00038
GO:0046599 regulation of centriole replication 15 3 0.15 0.00042

Factor 21

GO.ID Term Annotated Significant Expected classic
GO:0031424 keratinization 33 9 0.23 9.2e-13
GO:0043588 skin development 259 15 1.80 3.3e-10
GO:0030216 keratinocyte differentiation 122 11 0.85 8.2e-10
GO:0008544 epidermis development 287 14 1.99 1.2e-08
GO:0045104 intermediate filament cytoskeleton organ… 42 7 0.29 1.4e-08
GO:0050891 multicellular organismal water homeostas… 42 7 0.29 1.4e-08
GO:0045103 intermediate filament-based process 43 7 0.30 1.7e-08
GO:0030104 water homeostasis 45 7 0.31 2.4e-08
GO:0030855 epithelial cell differentiation 545 18 3.78 3.9e-08
GO:0009913 epidermal cell differentiation 182 11 1.26 5.5e-08

Factor 23

GO.ID Term Annotated Significant Expected classic
GO:0002376 immune system process 1951 62 20.07 7.3e-17
GO:0006955 immune response 1060 43 10.90 3.9e-15
GO:1903039 positive regulation of leukocyte cell-ce… 169 18 1.74 1.4e-13
GO:0007159 leukocyte cell-cell adhesion 305 22 3.14 7.6e-13
GO:0022409 positive regulation of cell-cell adhesio… 202 18 2.08 3.0e-12
GO:0002682 regulation of immune system process 1073 39 11.04 3.1e-12
GO:0046649 lymphocyte activation 599 29 6.16 3.3e-12
GO:0045321 leukocyte activation 707 31 7.27 7.0e-12
GO:0050870 positive regulation of T cell activation 159 16 1.64 8.1e-12
GO:1903037 regulation of leukocyte cell-cell adhesi… 277 20 2.85 8.8e-12

Factor 24

GO.ID Term Annotated Significant Expected classic
GO:0003341 cilium movement 69 3 0.07 4.0e-05
GO:0007018 microtubule-based movement 242 4 0.24 7.7e-05
GO:0060271 cilium assembly 272 4 0.27 0.00012
GO:0044782 cilium organization 291 4 0.29 0.00016
GO:0021591 ventricular system development 32 2 0.03 0.00044
GO:0120031 plasma membrane bounded cell projection … 443 4 0.44 0.00077
GO:0030031 cell projection assembly 450 4 0.44 0.00082
GO:0061886 negative regulation of mini excitatory p… 1 1 0.00 0.00098
GO:0099149 regulation of postsynaptic neurotransmit… 1 1 0.00 0.00098
GO:1903353 regulation of nucleus organization 1 1 0.00 0.00098

Factor 26

GO.ID Term Annotated Significant Expected classic
GO:0042403 thyroid hormone metabolic process 22 6 0.13 2.4e-09
GO:0006590 thyroid hormone generation 13 5 0.08 7.6e-09
GO:0018958 phenol-containing compound metabolic pro… 94 8 0.55 7.5e-08
GO:0006575 cellular modified amino acid metabolic p… 146 9 0.85 1.8e-07
GO:0042445 hormone metabolic process 144 8 0.84 2.0e-06
GO:0071675 regulation of mononuclear cell migration 41 4 0.24 9.4e-05
GO:0036343 psychomotor behavior 3 2 0.02 0.00010
GO:0061744 motor behavior 4 2 0.02 0.00020
GO:0065008 regulation of biological quality 3110 33 18.15 0.00026
GO:0090025 regulation of monocyte chemotaxis 22 3 0.13 0.00027

Factor 27

GO.ID Term Annotated Significant Expected classic
GO:0002376 immune system process 1951 41 17.25 8.0e-08
GO:0006952 defense response 1161 29 10.26 3.1e-07
GO:0045087 innate immune response 558 19 4.93 5.0e-07
GO:0006955 immune response 1060 27 9.37 5.8e-07
GO:0006954 inflammatory response 552 17 4.88 8.0e-06
GO:0097530 granulocyte migration 113 7 1.00 6.5e-05
GO:0042554 superoxide anion generation 28 4 0.25 0.00010
GO:0006801 superoxide metabolic process 55 5 0.49 0.00012
GO:1901292 nucleoside phosphate catabolic process 56 5 0.50 0.00013
GO:1990266 neutrophil migration 93 6 0.82 0.00018

Factor 28

GO.ID Term Annotated Significant Expected classic
GO:0050912 detection of chemical stimulus involved … 33 15 0.26 1.1e-23
GO:0001580 detection of chemical stimulus involved … 29 14 0.23 1.2e-22
GO:0050913 sensory perception of bitter taste 32 14 0.25 7.2e-22
GO:0050907 detection of chemical stimulus involved … 45 15 0.35 3.4e-21
GO:0050909 sensory perception of taste 51 15 0.40 3.1e-20
GO:0009593 detection of chemical stimulus 71 15 0.56 7.7e-18
GO:0050906 detection of stimulus involved in sensor… 105 16 0.83 1.5e-16
GO:0007606 sensory perception of chemical stimulus 141 15 1.11 3.2e-13
GO:0051606 detection of stimulus 193 16 1.52 2.5e-12
GO:0007186 G-protein coupled receptor signaling pat… 685 25 5.38 1.2e-10

Factor 29

GO.ID Term Annotated Significant Expected classic
GO:0002376 immune system process 1951 55 17.59 2.2e-15
GO:0045321 leukocyte activation 707 28 6.37 3.5e-11
GO:0001775 cell activation 821 30 7.40 4.5e-11
GO:0006955 immune response 1060 33 9.55 2.8e-10
GO:0002521 leukocyte differentiation 489 22 4.41 5.3e-10
GO:0046649 lymphocyte activation 599 24 5.40 8.3e-10
GO:0002682 regulation of immune system process 1073 32 9.67 1.6e-09
GO:0002684 positive regulation of immune system pro… 735 25 6.63 9.9e-09
GO:0002696 positive regulation of leukocyte activat… 259 15 2.33 1.3e-08
GO:0051251 positive regulation of lymphocyte activa… 225 14 2.03 1.6e-08

Factor 30

GO.ID Term Annotated Significant Expected classic
GO:0044782 cilium organization 291 47 12.12 1.1e-15
GO:0060271 cilium assembly 272 44 11.33 8.3e-15
GO:0120031 plasma membrane bounded cell projection … 443 49 18.46 4.5e-10
GO:0007017 microtubule-based process 639 62 26.62 4.8e-10
GO:0030031 cell projection assembly 450 49 18.75 7.8e-10
GO:0003341 cilium movement 69 17 2.87 2.2e-09
GO:0035082 axoneme assembly 60 15 2.50 1.6e-08
GO:0001578 microtubule bundle formation 88 17 3.67 1.1e-07
GO:0007018 microtubule-based movement 242 29 10.08 3.2e-07
GO:0000226 microtubule cytoskeleton organization 457 43 19.04 5.6e-07

Session information

sessionInfo()
#> R version 3.4.3 (2017-11-30)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#> 
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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    parallel  stats     graphics  grDevices utils     datasets 
#> [8] methods   base     
#> 
#> other attached packages:
#>  [1] org.Mm.eg.db_3.5.0   topGO_2.30.1         SparseM_1.77        
#>  [4] GO.db_3.5.0          AnnotationDbi_1.40.0 IRanges_2.12.0      
#>  [7] S4Vectors_0.16.0     Biobase_2.38.0       graph_1.56.0        
#> [10] BiocGenerics_0.24.0  ggplot2_3.1.0       
#> 
#> loaded via a namespace (and not attached):
#>  [1] xfun_0.4           lattice_0.20-35    colorspace_1.3-2  
#>  [4] htmltools_0.3.6    yaml_2.2.0         blob_1.1.0        
#>  [7] rlang_0.3.0.1      R.oo_1.21.0        pillar_1.2.1      
#> [10] glue_1.3.0         withr_2.1.2.9000   DBI_0.7           
#> [13] R.utils_2.6.0      bit64_0.9-7        bindrcpp_0.2      
#> [16] matrixStats_0.52.2 bindr_0.1          plyr_1.8.4        
#> [19] stringr_1.3.1      munsell_0.5.0      gtable_0.2.0      
#> [22] workflowr_1.0.1    flashier_0.1.0     R.methodsS3_1.7.1 
#> [25] evaluate_0.12      memoise_1.1.0      labeling_0.3      
#> [28] knitr_1.20.22      highr_0.7          Rcpp_1.0.0        
#> [31] scales_1.0.0       backports_1.1.2    bit_1.1-12        
#> [34] digest_0.6.18      stringi_1.2.4      dplyr_0.7.4       
#> [37] grid_3.4.3         rprojroot_1.3-2    tools_3.4.3       
#> [40] magrittr_1.5       lazyeval_0.2.1     tibble_1.4.2      
#> [43] RSQLite_2.0        whisker_0.3-2      pkgconfig_2.0.1   
#> [46] assertthat_0.2.0   rmarkdown_1.8      R6_2.3.0          
#> [49] git2r_0.21.0       compiler_3.4.3

This reproducible R Markdown analysis was created with workflowr 1.0.1