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library(tidyverse)
library(htmltools)
source('code/utils.R')
source('code/logistic_susie_vb.R')
source('code/logistic_susie_veb_boost.R')
source('code/load_gene_sets.R')
source('code/enrichment_pipeline.R')
Baboons were fed different diets for two years. Adipose, liver and muscle tissue were collected. Differential expression was conducted across the diet conditions.
genesets <- load_gene_sets()
de.adipose <- read.table('data/wenhe_baboon_diet/DE_lrt_adipose.txt')
de.liver <- read.table('data/wenhe_baboon_diet/DE_lrt_liver.txt')
de.muscle <- read.table('data/wenhe_baboon_diet/DE_lrt_muscle.txt')
de <- bind_rows(
rownames_to_column(de.adipose) %>% mutate(tissue='Adipose'),
rownames_to_column(de.liver) %>% mutate(tissue='Liver'),
rownames_to_column(de.muscle) %>% mutate(tissue='Muscle')) %>%
rename(gene=rowname)
hs <- org.Hs.eg.db::org.Hs.eg.db
gene_symbols <- unique(de$gene)
symbol2entrez <- AnnotationDbi::select(
hs, keys=gene_symbols,
columns=c('ENTREZID', 'SYMBOL'),
keytype = 'SYMBOL')
add_names = function(l, n){
names(l) <- n
return(l)
}
data <- de %>%
rename(SYMBOL=gene) %>%
left_join(symbol2entrez, by='SYMBOL') %>%
relocate(ENTREZID, .after=SYMBOL) %>%
mutate( # set default columns
beta = logFC,
se = 0,
threshold.on = PValue
) %>%
group_by(tissue) %>%
group_map(~ .x, .keep = T) %>%
add_names(map_chr(., ~pluck(.x, 'tissue')[1]))
# fit logistic susie
do_logistic_susie_cached = function(data,
db,
thresh,
prefix=''){
res <- xfun::cache_rds({
purrr::map_dfr(
names(data),
~do_logistic_susie(.x, db, thresh, genesets, data))
},
dir = params$cache_dir,
file=paste0(prefix, 'logistic_susie_', db, '_', thresh),
hash = list(data, db, thresh, prefix))
}
params.genesets <- eval(parse(text=params$genesets))
params.thresh <- eval(parse(text=params$thresh))
fits <- map_dfr(params.genesets, ~do_logistic_susie_cached(data, .x, params.thresh))
# fit ora
do_ora_cached = function(data, db, thresh, prefix='', ...){
res <- xfun::cache_rds({
purrr::map_dfr(names(data), ~do_ora(.x, db, thresh, genesets, data))
}, dir = params$cache_dir, file=paste0(prefix, 'ora_', db, '_', thresh), ...)
}
ora <- map_dfr(params.genesets, ~do_ora_cached(data, .x, params.thresh))
mean.gene.prop = function(l){
purrr::map_dbl(3:10, ~get_y(l, 10^(-.x)) %>% mean())
}
thresh <- map_dbl(1:10, ~10**-.x)
.prop.ones = function(experiment){
map_dbl(thresh, ~ prep_binary_data(
genesets[['gobp']], data[[experiment]], thresh=.x)$y %>% mean())
}
prop.ones <- xfun::cache_rds({map_dfc(names(data), ~.prop.ones(.x))},
dir=params$cache_dir,
file='threshold_sensitivity')
colnames(prop.ones) <- names(data)
prop.ones <- prop.ones %>% mutate(thresh = thresh)
prop.ones %>%
pivot_longer(one_of(names(data))) %>%
group_by(name) %>%
mutate(value = value) %>%
ggplot(aes(x=factor(-log10(thresh)), y=value)) +
geom_boxplot() +
labs(
y = 'Proportions of genes in gene list',
title = 'Sensitivity to thresholding'
)
Colors represent enrichment/depletion detected by Fishers exact test (Benjamini Hochberg corrected p-values < \(0.05\)). Gene sets that belong to a SuSiE credible set are circled.
get_ora_enrichments = function(tbl){
tbl %>% mutate(
padj = p.adjust(pFishersExact),
result = case_when(
padj < 0.05 & oddsRatio < 1 ~ 'depleted',
padj < 0.05 & oddsRatio > 1 ~ 'enriched',
TRUE ~ 'not significant'
)
)
}
# plot all enrichments, highlight gene sets in credible set
csdat <- res2 %>%
filter(in_cs, active_cs)
res %>%
group_by(experiment, db) %>%
get_ora_enrichments %>%
ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
geom_point() +
geom_point(
csdat,
mapping=aes(x=log10(oddsRatio), y=-log10(pFishersExact)),
color='black', pch=21, size=5) +
scale_color_manual(values = c('depleted' = 'coral',
'enriched' = 'dodgerblue',
'not significant' = 'grey')) +
facet_wrap(vars(db))
alpha
is the posterior probability of SuSiE including this gene set in this component which is different from PIP (probability of SuSiE including this gene set in ANY component)beta
posterior mean/standard error of posterior mean for effect size. Standard errors are likely too small.oddsRatio, pHypergeometric, pFishersExact
construct a contingency table (gene list membersip) x (gene set membership), estimate the oddsRatio
gives the odds of being in the gene list conditional on being in the gene set / odds of being in the gene list conditional on NOT being in the gene set. pHypergeometric
and pFishersExact
are pvalues from 1 and 2 sided test respectively.experiments <- unique(res$experiment)
do.experiment.volcano = function(this_experiment){
res %>%
filter(experiment == this_experiment) %>%
group_by(db) %>%
get_ora_enrichments %>%
ggplot(aes(x=log10(oddsRatio), y=-log10(pFishersExact), color=result)) +
geom_point() +
geom_point(
csdat %>% filter(experiment == this_experiment),
mapping=aes(x=log10(oddsRatio), y=-log10(pFishersExact)),
color='black', pch=21, size=5) +
scale_color_manual(values = c('depleted' = 'coral',
'enriched' = 'dodgerblue',
'not significant' = 'grey')) +
facet_wrap(vars(db)) +
labs(title = this_experiment)
}
for (i in 1:length(experiments)){
this_experiment <- experiments[i]
cat("\n")
cat("###", this_experiment, "\n") # Create second level headings with the names.
do.experiment.volcano(this_experiment) %>% print()
cat("\n\n")
for(db in names(html_tables[[this_experiment]])){
cat("####", db, "\n") # Create second level headings with the names.
to_print <- html_tables[[this_experiment]][[db]] %>% distinct()
to_print %>% report_susie_credible_sets() %>% htmltools::HTML() %>% print()
cat("\n")
}}
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0072376 | protein activation cascade | 1 | 2.98 | 0.24 | 1.46e-24 | 1.46e-24 | 30 | 72 | 20.7 |
L2 | |||||||||
GO:0019752 | carboxylic acid metabolic process | 0.998 | 1.33 | 0.0819 | 3.28e-20 | 3.28e-20 | 87 | 811 | 3.79 |
L3 | |||||||||
GO:0010466 | negative regulation of peptidase activity | 0.827 | 1.67 | 0.17 | 2.88e-15 | 2.88e-15 | 33 | 171 | 6.92 |
GO:0010951 | negative regulation of endopeptidase activity | 0.173 | 1.66 | 0.171 | 9.49e-15 | 9.49e-15 | 32 | 167 | 6.85 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0004867 | serine-type endopeptidase inhibitor activity | 1 | 2.86 | 0.272 | 9.13e-18 | 9.13e-18 | 22 | 55 | 18.8 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
hsa04610 | Complement and coagulation cascades | 1 | 3.03 | 0.243 | 6.37e-23 | 6.37e-23 | 31 | 68 | 18.4 |
L2 | |||||||||
hsa04950 | Maturity onset diabetes of the young | 1 | 3.4 | 0.501 | 1.68e-08 | 1.68e-08 | 9 | 16 | 26.1 |
L3 | |||||||||
hsa04976 | Bile secretion | 1 | 2.15 | 0.28 | 7.52e-10 | 7.52e-10 | 17 | 55 | 9.3 |
L4 | |||||||||
hsa00830 | Retinol metabolism | 1 | 2.8 | 0.393 | 1.9e-08 | 1.9e-08 | 11 | 26 | 15 |
L5 | |||||||||
hsa04979 | Cholesterol metabolism | 1 | 1.85 | 0.308 | 3.43e-07 | 3.43e-07 | 13 | 47 | 7.83 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0006936 | muscle contraction | 0.982 | 0.801 | 0.118 | 5.88e-17 | 1.04e-16 | 130 | 283 | 3.73 |
GO:0070252 | actin-mediated cell contraction | 0.00797 | 1.15 | 0.194 | 4.26e-13 | 4.26e-13 | 58 | 102 | 5.69 |
L2 | |||||||||
GO:0034641 | cellular nitrogen compound metabolic process | 1 | -0.497 | 0.0302 | 1 | 6.58e-27 | 970 | 5180 | 0.968 |
L3 | |||||||||
GO:0048513 | animal organ development | 1 | 0.429 | 0.0403 | 6.72e-22 | 1.22e-21 | 804 | 2610 | 2.22 |
L4 | |||||||||
GO:0006955 | immune response | 0.999 | 0.424 | 0.0531 | 6.26e-18 | 1.11e-17 | 483 | 1480 | 2.27 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0038023 | signaling receptor activity | 0.905 | 0.702 | 0.0738 | 9.03e-21 | 1.23e-20 | 283 | 745 | 2.81 |
GO:0004888 | transmembrane signaling receptor activity | 0.0515 | 0.776 | 0.0845 | 5.76e-21 | 7.43e-21 | 229 | 565 | 3.09 |
GO:0060089 | molecular transducer activity | 0.0435 | 0.658 | 0.0716 | 2.21e-19 | 3.07e-19 | 294 | 797 | 2.68 |
L2 | |||||||||
GO:0003676 | nucleic acid binding | 1 | -0.424 | 0.0388 | 1 | 1.01e-23 | 537 | 3180 | 0.846 |
L3 | |||||||||
GO:0048018 | receptor ligand activity | 0.882 | 0.758 | 0.118 | 1.74e-10 | 2.56e-10 | 114 | 286 | 2.93 |
GO:0030545 | receptor regulator activity | 0.118 | 0.695 | 0.114 | 1.08e-09 | 1.41e-09 | 119 | 310 | 2.75 |
L4 | |||||||||
GO:0015267 | channel activity | 0.227 | 0.603 | 0.114 | 6.36e-10 | 9.14e-10 | 120 | 311 | 2.78 |
GO:0022803 | passive transmembrane transporter activity | 0.227 | 0.603 | 0.114 | 6.36e-10 | 9.14e-10 | 120 | 311 | 2.78 |
GO:0005244 | voltage-gated ion channel activity | 0.165 | 0.865 | 0.168 | 2.81e-08 | 3.5e-08 | 61 | 137 | 3.5 |
GO:0022832 | voltage-gated channel activity | 0.165 | 0.865 | 0.168 | 2.81e-08 | 3.5e-08 | 61 | 137 | 3.5 |
GO:0022838 | substrate-specific channel activity | 0.124 | 0.602 | 0.117 | 1.14e-09 | 1.49e-09 | 115 | 297 | 2.79 |
GO:0005216 | ion channel activity | 0.0301 | 0.577 | 0.118 | 6.41e-09 | 1.1e-08 | 110 | 288 | 2.72 |
GO:0022836 | gated channel activity | 0.0206 | 0.619 | 0.13 | 1.19e-08 | 1.6e-08 | 94 | 238 | 2.87 |
GO:0022843 | voltage-gated cation channel activity | 0.016 | 0.923 | 0.199 | 2.05e-07 | 2.53e-07 | 45 | 95 | 3.92 |
GO:0005261 | cation channel activity | 0.0125 | 0.626 | 0.134 | 2.83e-08 | 5.04e-08 | 88 | 222 | 2.88 |
GO:0022839 | ion gated channel activity | 0.00409 | 0.583 | 0.132 | 8.84e-08 | 1.39e-07 | 89 | 230 | 2.77 |
L5 | |||||||||
GO:0008092 | cytoskeletal protein binding | 0.933 | 0.384 | 0.0704 | 2.31e-07 | 4.03e-07 | 255 | 832 | 1.99 |
GO:0003779 | actin binding | 0.0578 | 0.503 | 0.104 | 1.3e-06 | 2.03e-06 | 124 | 364 | 2.28 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
hsa04514 | Cell adhesion molecules (CAMs) | 0.999 | 1.07 | 0.192 | 2.56e-08 | 3.18e-08 | 52 | 106 | 4.06 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0072376 | protein activation cascade | 1 | 2.55 | 0.237 | 4.12e-22 | 4.12e-22 | 34 | 72 | 14.6 |
L2 | |||||||||
GO:0009063 | cellular amino acid catabolic process | 0.976 | 2.15 | 0.196 | 3.74e-21 | 3.74e-21 | 40 | 107 | 9.83 |
GO:1901606 | alpha-amino acid catabolic process | 0.0241 | 2.28 | 0.214 | 1.61e-20 | 1.61e-20 | 36 | 89 | 11.1 |
L3 | |||||||||
GO:0090304 | nucleic acid metabolic process | 1 | -0.844 | 0.0421 | 1 | 8.07e-24 | 138 | 4100 | 0.454 |
L4 | |||||||||
GO:0006641 | triglyceride metabolic process | 0.928 | 1.64 | 0.237 | 5.7e-12 | 5.7e-12 | 25 | 78 | 7.62 |
GO:0006639 | acylglycerol metabolic process | 0.0396 | 1.42 | 0.22 | 1.16e-10 | 1.16e-10 | 26 | 95 | 6.09 |
GO:0006638 | neutral lipid metabolic process | 0.0329 | 1.41 | 0.219 | 1.49e-10 | 1.49e-10 | 26 | 96 | 6 |
L5 | |||||||||
GO:0030855 | epithelial cell differentiation | 1 | 1.11 | 0.106 | 2.58e-09 | 2.8e-09 | 64 | 463 | 2.65 |
L6 | |||||||||
GO:0016101 | diterpenoid metabolic process | 0.591 | 1.63 | 0.262 | 9.2e-10 | 9.2e-10 | 20 | 63 | 7.48 |
GO:0001523 | retinoid metabolic process | 0.309 | 1.66 | 0.272 | 1.33e-09 | 1.33e-09 | 19 | 58 | 7.82 |
GO:0006721 | terpenoid metabolic process | 0.0979 | 1.51 | 0.254 | 5.48e-09 | 5.48e-09 | 20 | 69 | 6.56 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
GO:0015294 | solute:cation symporter activity | 0.933 | 1.74 | 0.237 | 1.14e-10 | 1.14e-10 | 23 | 75 | 7.12 |
GO:0015293 | symporter activity | 0.0356 | 1.42 | 0.205 | 1.88e-10 | 1.88e-10 | 28 | 111 | 5.45 |
GO:0015370 | solute:sodium symporter activity | 0.0311 | 2.01 | 0.294 | 2.92e-10 | 2.92e-10 | 18 | 48 | 9.62 |
L2 | |||||||||
GO:0003676 | nucleic acid binding | 1 | -0.981 | 0.0487 | 1 | 1.35e-25 | 87 | 3180 | 0.374 |
L3 | |||||||||
GO:0004866 | endopeptidase inhibitor activity | 0.56 | 1.47 | 0.202 | 3.07e-09 | 3.07e-09 | 26 | 109 | 5.05 |
GO:0030414 | peptidase inhibitor activity | 0.348 | 1.45 | 0.201 | 4.64e-09 | 4.64e-09 | 26 | 111 | 4.93 |
GO:0061135 | endopeptidase regulator activity | 0.0903 | 1.39 | 0.198 | 1.25e-08 | 1.25e-08 | 26 | 116 | 4.66 |
L4 | |||||||||
GO:0019842 | vitamin binding | 1 | 1.49 | 0.199 | 9.57e-10 | 9.57e-10 | 27 | 111 | 5.19 |
L5 | |||||||||
GO:0004252 | serine-type endopeptidase activity | 0.929 | 1.35 | 0.199 | 6.95e-09 | 6.95e-09 | 26 | 113 | 4.82 |
GO:0017171 | serine hydrolase activity | 0.0422 | 1.18 | 0.186 | 7.16e-08 | 7.16e-08 | 27 | 134 | 4.07 |
GO:0008236 | serine-type peptidase activity | 0.0283 | 1.18 | 0.189 | 1.46e-07 | 1.46e-07 | 26 | 130 | 4.02 |
geneSet | description | alpha | beta | beta.se | pHypergeometric | pFishersExact | overlap | geneSetSize | oddsRatio |
---|---|---|---|---|---|---|---|---|---|
L1 | |||||||||
hsa04610 | Complement and coagulation cascades | 1 | 2.71 | 0.242 | 1.45e-21 | 1.45e-21 | 35 | 68 | 14.6 |
L2 | |||||||||
hsa00260 | Glycine, serine and threonine metabolism | 0.987 | 1.64 | 0.344 | 1.6e-08 | 1.6e-08 | 15 | 35 | 9.85 |
hsa04950 | Maturity onset diabetes of the young | 0.00463 | 1.91 | 0.574 | 0.000108 | 0.000108 | 7 | 16 | 10 |
L3 | |||||||||
hsa04979 | Cholesterol metabolism | 1 | 1.95 | 0.295 | 2.49e-07 | 2.49e-07 | 16 | 47 | 6.78 |
L4 | |||||||||
hsa00380 | Tryptophan metabolism | 1 | 2.31 | 0.36 | 2.14e-08 | 2.14e-08 | 14 | 31 | 10.8 |
L5 | |||||||||
hsa01230 | Biosynthesis of amino acids | 1 | 1.55 | 0.256 | 9.31e-09 | 9.31e-09 | 21 | 65 | 6.33 |
sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats graphics grDevices datasets utils methods base
#>
#> other attached packages:
#> [1] kableExtra_1.3.4 BiocGenerics_0.40.0 htmltools_0.5.2
#> [4] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8
#> [7] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
#> [10] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1
#>
#> loaded via a namespace (and not attached):
#> [1] colorspace_2.0-3 ellipsis_0.3.2 rprojroot_2.0.2
#> [4] XVector_0.34.0 fs_1.5.2 rstudioapi_0.13
#> [7] farver_2.1.0 bit64_4.0.5 AnnotationDbi_1.56.2
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