inst/extdata/pathwayDB/pathways.md

In Jasondd66/covid_19bioMarkers: Performs common bioinformatics analyses

Steps to reproduce pathwayDB

• downloaded from https://amp.pharm.mssm.edu/Enrichr/#stats on February 20, 2020 and converted them to .csv:
  • each row of the file is a pathway name followed by the gene symbols that belong to that pathway
  • applying read.delim() on the .txt files resulted in some issues (genes names going to the next line down)

databaseFiles <- c("BioCarta_2016.csv", "KEGG_2019_Human.csv", "Reactome_2016.csv", "WikiPathways_2019_Human.csv")
pathwayDB <- lapply(databaseFiles, function(pathwayName){
  cat("Processing: ", pathwayName, fill = TRUE)
  dat <- read.csv(here::here("inst", "extdata", "pathwayDB", "data", pathwayName), header = FALSE)
  dat[dat == ""] <- NA
  dat %>% 
    gather(Members, Genes, -V1) %>% 
    filter(!is.na(Genes)) %>% 
    rename(Pathways = V1) %>% 
    dplyr::select(Pathways, Genes) %>% 
    mutate(DB = gsub(".csv", "", pathwayName))
}) %>% 
  do.call(rbind, .)

## Processing:  BioCarta_2016.csv
## Processing:  KEGG_2019_Human.csv
## Processing:  Reactome_2016.csv
## Processing:  WikiPathways_2019_Human.csv

Pathway DB characteristics

Which DB has the most genesets?

pathwayDB %>% 
  dplyr::select(DB, Pathways) %>% 
  group_by(DB) %>% 
  summarise(n = n_distinct(Pathways)) %>% 
  ggplot(aes(x = reorder(DB, -n), y = n)) +
  geom_bar(stat = "identity") +
  ylab("Number of pathways per DB") +
  xlab("DB") +
  theme_classic()

Reactome has the most genesets whereas BioCarta has the least number of genesets.

Which DB captures the most number of unique genes?

pathwayDB %>% 
  group_by(DB) %>% 
  summarise(n = n_distinct(Genes)) %>% 
  ggplot(aes(x = reorder(DB, -n), y = n)) +
  geom_bar(stat = "identity") +
  ylab("Number of genesets") +
  xlab("DB") +
  theme_classic()

BioCarta captures the least number of unique genes, whereas the remianing three capture >5K genes.

Which pathway is the largest per DB?

pathwayTally <- pathwayDB %>% 
  group_by(DB, Pathways) %>% 
  summarise(n = n())

pathwayTally %>% 
  ggplot(aes(x = n)) +
  geom_histogram() +
  facet_wrap(vars(DB), scales = "free") + 
  scale_y_log10() +
  ylab("Frequency of genesets with a given number of genes") +
  xlab("Number of genes") +
  theme_classic()

Genesets with the most number of gene members (n)

| DB | Pathways | n | | :------------------------ | :----------------------------------------------------- | ---: | | BioCarta_2016 | MAPKinase Signaling Pathway Homo sapiens h mapkPathway | 56 | | KEGG_2019_Human | Pathways in cancer | 530 | | Reactome_2016 | Signal Transduction Homo sapiens R-HSA-162582 | 2465 | | WikiPathways_2019_Human | PI3K-Akt Signaling Pathway WP4172 | 340 |

Genesets with the least number of gene members (n)

| DB | Pathways | n | | :------------------------ | :-------------------------------------------------------------------------- | -: | | BioCarta_2016 | Acetylation and Deacetylation of RelA in Nucleus Homo sapiens h RELAPathway | 5 | | KEGG_2019_Human | Caffeine metabolism | 5 | | Reactome_2016 | Abacavir metabolism Homo sapiens R-HSA-2161541 | 5 | | WikiPathways_2019_Human | Catalytic cycle of mammalian Flavin-containing MonoOxygenases (FMOs) WP688 | 5 |

Save package data

usethis::use_data(pathwayDB, overwrite = TRUE)

## ✔ Setting active project to '/Users/asingh/Documents/omicsBioAnalytics'
## ✔ Saving 'pathwayDB' to 'data/pathwayDB.rda'

Jasondd66/covid_19bioMarkers documentation built on Dec. 18, 2021, 12:33 a.m.