example_yusha_sc

Last updated: 2022-07-15

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Knit directory: logistic-susie-gsea/

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Load data

source('code/load_data.R')

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──

✔ ggplot2 3.3.6     ✔ purrr   0.3.4
✔ tibble  3.1.7     ✔ dplyr   1.0.9
✔ tidyr   1.2.0     ✔ stringr 1.4.0
✔ readr   2.1.2     ✔ forcats 0.5.1

── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(gseasusie)

# save output to a folder... helps for running many factors
cache_rds = purrr::partial(xfun::cache_rds, dir='cache/sc_tumor/')

driver = function(gs, experiment){
  dat <- gseasusie::prep_binary_data(gs, data[[experiment]])
  ora <- gseasusie::fit_ora(dat$X, dat$y)
  # add description
  ora <- ora %>%
    dplyr::left_join(gs$geneSetDes)
  fit <- gseasusie::fit_logistic_susie_veb_boost(dat$X, dat$y)
  return(list(fit=fit, ora=ora))
}

driver_cached = function(prefix, gs, experiment){
  file = paste0(prefix, '_', gs$db, '_', experiment, '.rds')
  print(file)
  cache_rds(driver(gs, experiment), file=file)
}

data  <- load_sc_tumor_hnscc()

'select()' returned 1:many mapping between keys and columns

go <- gseasusie::load_all_go()

loading gene set from webgestaltr: geneontology_Biological_Process

loading gene set from webgestaltr: geneontology_Molecular_Function

loading gene set from webgestaltr: geneontology_Cellular_Component

hnscc_res <- purrr::map(names(data), ~driver_cached('hnscc', go, .x))

[1] "hnscc_all_go_factor10.rds"
[1] "hnscc_all_go_factor11.rds"
[1] "hnscc_all_go_factor12.rds"
[1] "hnscc_all_go_factor13.rds"
[1] "hnscc_all_go_factor14.rds"
[1] "hnscc_all_go_factor15.rds"
[1] "hnscc_all_go_factor16.rds"
[1] "hnscc_all_go_factor17.rds"
[1] "hnscc_all_go_factor18.rds"
[1] "hnscc_all_go_factor19.rds"
[1] "hnscc_all_go_factor2.rds"
[1] "hnscc_all_go_factor20.rds"
[1] "hnscc_all_go_factor21.rds"
[1] "hnscc_all_go_factor22.rds"
[1] "hnscc_all_go_factor23.rds"
[1] "hnscc_all_go_factor24.rds"
[1] "hnscc_all_go_factor3.rds"
[1] "hnscc_all_go_factor4.rds"
[1] "hnscc_all_go_factor5.rds"
[1] "hnscc_all_go_factor6.rds"
[1] "hnscc_all_go_factor7.rds"
[1] "hnscc_all_go_factor8.rds"
[1] "hnscc_all_go_factor9.rds"

names(hnscc_res) <- names(data)

data  <- load_sc_tumor_pdac()

'select()' returned 1:many mapping between keys and columns

pdac_res <- purrr::map(names(data), ~driver_cached('pdac', go, .x))

[1] "pdac_all_go_factor10.rds"
[1] "pdac_all_go_factor11.rds"
[1] "pdac_all_go_factor15.rds"
[1] "pdac_all_go_factor16.rds"
[1] "pdac_all_go_factor17.rds"
[1] "pdac_all_go_factor19.rds"
[1] "pdac_all_go_factor2.rds"
[1] "pdac_all_go_factor20.rds"
[1] "pdac_all_go_factor24.rds"
[1] "pdac_all_go_factor25.rds"
[1] "pdac_all_go_factor26.rds"
[1] "pdac_all_go_factor28.rds"
[1] "pdac_all_go_factor3.rds"
[1] "pdac_all_go_factor30.rds"
[1] "pdac_all_go_factor32.rds"
[1] "pdac_all_go_factor4.rds"
[1] "pdac_all_go_factor5.rds"
[1] "pdac_all_go_factor6.rds"
[1] "pdac_all_go_factor7.rds"
[1] "pdac_all_go_factor8.rds"

results <- hnscc_res
experiments <- names(results)

safe_static_table <- purrr::safely(
  gseasusie::static_table,
  otherwise = 'nothing to report')

for(this_experiment in experiments){
  sub_res <- results[[this_experiment]]
  volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  results[[this_experiment]]$volcano <- volcano
  
  table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  results[[this_experiment]]$table <- table
}

cat('\n')

cat('##', 'HNSCC')

HNSCC

for(this_experiment in experiments){
  cat('\n')
  cat('###', this_experiment)

  #sub_res <- results[[this_experiment]]
  #volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  print(results[[this_experiment]]$volcano)
  
  cat("\n\n")
  #table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  print(results[[this_experiment]]$table)
}

factor10

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0070062	extracellular exosome	1290	71	2.4	1.93	0.347	0.348	20.7	1
GO:0043230	extracellular organelle	1290	71	2.4	1.93	0.326	0.327	20.6	2
GO:1903561	extracellular vesicle	1290	71	2.4	1.93	0.326	0.327	20.6	3
L1
GO:0006735	NADH regeneration	19	8	5.44	4.29	0.24	0.241	9.36	12
GO:0061621	canonical glycolysis	19	8	5.44	4.29	0.24	0.241	9.36	13
GO:0061718	glucose catabolic process to pyruvate	19	8	5.44	4.29	0.24	0.241	9.36	14
GO:0061615	glycolytic process through fructose-6-phosphate	20	8	5.32	4.15	0.118	0.118	9.15	18
GO:0061620	glycolytic process through glucose-6-phosphate	20	8	5.32	4.15	0.118	0.118	9.15	19
L3
GO:1900115	extracellular regulation of signal transduction	18	7	5.24	5.33	0.5	0.5	7.96	35
GO:1900116	extracellular negative regulation of signal transduction	18	7	5.24	5.33	0.5	0.5	7.96	36

factor11

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0048019	receptor antagonist activity	19	10	6.32	6.17	0.983	0.983	13.5	1

factor12

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0044421	extracellular region part	1720	81	2.25	1.91	1	1	19.7	1
L1
GO:0009812	flavonoid metabolic process	7	5	7.19	7.53	0.999	0.999	7.51	24

factor13

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor14

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0051301	cell division	411	73	4.36	2.77	1	1	54.8	2
L1
GO:0007059	chromosome segregation	217	53	4.68	2.01	0.119	0.12	46.1	6
GO:0000819	sister chromatid segregation	143	42	4.91	2.39	0.85	0.85	39.8	11
L3
GO:0005874	microtubule	247	42	3.88	2.11	1	1	29.1	21

factor15

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor16

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0070268	cornification	61	15	4.31	4.15	0.982	0.982	13	1

factor17

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor18

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor19

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0070062	extracellular exosome	1290	72	2.46	2.19	0.347	0.348	21.6	1
GO:0043230	extracellular organelle	1290	72	2.45	2.18	0.326	0.327	21.5	2
GO:1903561	extracellular vesicle	1290	72	2.45	2.18	0.326	0.327	21.5	3
L1
GO:0070069	cytochrome complex	23	9	5.28	5.67	1	1	10.2	20
L3
GO:0042613	MHC class II protein complex	12	6	5.89	5.56	0.987	0.987	7.7	55

factor2

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006805	xenobiotic metabolic process	60	14	4.23	4.08	1	1	11.9	2

factor20

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0031012	extracellular matrix	215	42	4.1	2.94	1	1	31.5	1
L2
GO:0030198	extracellular matrix organization	183	38	4.17	2.19	0.941	0.941	29.4	4
GO:0043062	extracellular structure organization	212	39	3.96	2.02	0.0589	0.0597	28.1	5

factor21

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor22

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor23

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0005615	extracellular space	1630	93	2.61	2.01	1	1	27.8	1
L1
GO:0031424	keratinization	69	23	4.94	4.1	0.432	0.432	22.8	7
GO:0070268	cornification	61	22	5.11	4.26	0.568	0.569	22.7	8

factor24

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0060337	type I interferon signaling pathway	64	25	5.37	5.21	0.478	0.478	27.1	5
GO:0071357	cellular response to type I interferon	64	25	5.37	5.21	0.478	0.478	27.1	6
L2
GO:0042613	MHC class II protein complex	12	7	6.32	6.28	0.986	0.986	9.4	65

factor3

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L2
GO:0005576	extracellular region	1980	105	2.85	2.19	1	1	32.2	1
L1
GO:0042611	MHC protein complex	17	8	5.69	5.27	0.995	0.995	9.75	33
L3
GO:1900115	extracellular regulation of signal transduction	18	8	5.54	3.95	0.497	0.497	9.5	38
GO:1900116	extracellular negative regulation of signal transduction	18	8	5.54	3.95	0.497	0.497	9.5	39

factor4

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	19	10	6.15	6.05	0.5	0.5	13	1
GO:0098553	lumenal side of endoplasmic reticulum membrane	19	10	6.15	6.05	0.5	0.5	13	2
L2
GO:1900118	negative regulation of execution phase of apoptosis	16	8	5.97	5.88	0.992	0.992	10.3	5

factor5

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0006261	DNA-dependent DNA replication	116	36	4.91	4.57	1	1	34.5	10
L3
GO:0000280	nuclear division	273	43	3.7	2.88	0.998	0.998	27.9	16
L2
GO:0006323	DNA packaging	98	24	4.31	3.72	1	1	20.1	35
L4
GO:0009263	deoxyribonucleotide biosynthetic process	12	6	5.78	6.21	0.998	0.998	7.5	159

factor6

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

factor7

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0070469	respiratory chain	77	26	5.11	4.93	1	1	26.7	1

factor8

Version	Author	Date
eb48f62	karltayeb	2022-07-14

geneSet	description	geneSetSize	overlap	log2OR	effect	alpha	pip	nlog10pFishersExact	fisherRank
L1
GO:0070431	nucleotide-binding oligomerization domain containing 2 signaling pathway	5	4	7.83	7.8	0.993	0.993	6.32	31

factor9

Version	Author	Date
eb48f62	karltayeb	2022-07-14

[1] “nothing to report”

results <- pdac_res
experiments <- names(results)

for(this_experiment in experiments){
  sub_res <- results[[this_experiment]]
  volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  results[[this_experiment]]$volcano <- volcano
  
  table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  results[[this_experiment]]$table <- table
}

cat('\n')

cat('##', 'PDAC')

PDAC

for(this_experiment in experiments){
  cat('\n')
  cat('###', this_experiment)
  cat('\n')

  #sub_res <- results[[this_experiment]]
  #volcano <- gseasusie::enrichment_volcano(fit=sub_res$fit, ora=sub_res$ora)
  print(results[[this_experiment]]$volcano)
  
  cat("\n\n")
  #table <- safe_static_table(sub_res$fit, sub_res$ora)$result
  print(results[[this_experiment]]$table)
}

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 utils     datasets  methods   base     

other attached packages:
 [1] gseasusie_0.0.0.9000 forcats_0.5.1        stringr_1.4.0       
 [4] dplyr_1.0.9          purrr_0.3.4          readr_2.1.2         
 [7] tidyr_1.2.0          tibble_3.1.7         ggplot2_3.3.6       
[10] tidyverse_1.3.1     

loaded via a namespace (and not attached):
  [1] matrixStats_0.62.0     bitops_1.0-7           fs_1.5.2              
  [4] lubridate_1.8.0        bit64_4.0.5            webshot_0.5.3         
  [7] httr_1.4.3             rprojroot_2.0.3        GenomeInfoDb_1.30.1   
 [10] data.tree_1.0.0        tools_4.1.2            backports_1.4.1       
 [13] bslib_0.3.1            utf8_1.2.2             R6_2.5.1              
 [16] DBI_1.1.2              BiocGenerics_0.40.0    colorspace_2.0-3      
 [19] withr_2.5.0            tidyselect_1.1.2       bit_4.0.4             
 [22] compiler_4.1.2         git2r_0.30.1           VEB.Boost_0.0.0.9037  
 [25] cli_3.3.0              rvest_1.0.2            Biobase_2.54.0        
 [28] xml2_1.3.3             labeling_0.4.2         sass_0.4.1            
 [31] scales_1.2.0           mvtnorm_1.1-3          systemfonts_1.0.4     
 [34] digest_0.6.29          spatstat.utils_2.3-1   svglite_2.1.0         
 [37] rmarkdown_2.14         XVector_0.34.0         pkgconfig_2.0.3       
 [40] htmltools_0.5.2        highr_0.9              dbplyr_2.2.0          
 [43] fastmap_1.1.0          rlang_1.0.2            readxl_1.4.0          
 [46] rstudioapi_0.13        RSQLite_2.2.14         farver_2.1.0          
 [49] jquerylib_0.1.4        generics_0.1.2         jsonlite_1.8.0        
 [52] mr.ash.alpha_0.1-42    RCurl_1.98-1.7         magrittr_2.0.3        
 [55] kableExtra_1.3.4       GenomeInfoDbData_1.2.7 Matrix_1.4-1          
 [58] Rcpp_1.0.8.3           munsell_0.5.0          S4Vectors_0.32.4      
 [61] fansi_1.0.3            lifecycle_1.0.1        stringi_1.7.6         
 [64] whisker_0.4            yaml_2.3.5             zlibbioc_1.40.0       
 [67] org.Hs.eg.db_3.14.0    grid_4.1.2             blob_1.2.3            
 [70] parallel_4.1.2         promises_1.2.0.1       crayon_1.5.1          
 [73] lattice_0.20-45        Biostrings_2.62.0      haven_2.5.0           
 [76] hms_1.1.1              KEGGREST_1.34.0        knitr_1.39            
 [79] pillar_1.7.0           stats4_4.1.2           reprex_2.0.1          
 [82] glue_1.6.2             evaluate_0.15          emulator_1.2-21       
 [85] modelr_0.1.8           vctrs_0.4.1            png_0.1-7             
 [88] tzdb_0.3.0             httpuv_1.6.5           cellranger_1.1.0      
 [91] gtable_0.3.0           assertthat_0.2.1       cachem_1.0.6          
 [94] xfun_0.31              broom_0.8.0            later_1.3.0           
 [97] viridisLite_0.4.0      AnnotationDbi_1.56.2   memoise_2.0.1         
[100] IRanges_2.28.0         workflowr_1.7.0        ellipsis_0.3.2

example_yusha_sc_tumor

karltayeb

2022-07-13

Load data

HNSCC

factor10

factor11

factor12

factor13

factor14

factor15

factor16

factor17

factor18

factor19

factor2

factor20

factor21

factor22

factor23

factor24

factor3

factor4

factor5

factor6

factor7

factor8

factor9

PDAC