GO.db: why does GOCCCHILDREN$"GO:0005575" work, but not GOCCCHILDREN$go when go="GO:0005575"
2
0
Entering edit mode
8.9 years ago
library("GO.db")
GOCCCHILDREN$"GO:0005575"
        is_a         is_a         is_a         is_a         is_a         is_a
"GO:0016020" "GO:0005576" "GO:0005581" "GO:0005623" "GO:0009295" "GO:0019012"
        is_a         is_a         is_a         is_a         is_a         is_a
"GO:0030054" "GO:0031012" "GO:0031974" "GO:0032991" "GO:0039679" "GO:0043226"
        is_a         is_a         is_a         is_a         is_a         is_a
"GO:0044420" "GO:0044421" "GO:0044422" "GO:0044423" "GO:0044425" "GO:0044456"
        is_a         is_a         is_a         is_a
"GO:0044464" "GO:0045202" "GO:0055044" "GO:0097423"
go <- "GO:0005575"
GOCCCHILDREN$go
NULL

If this isn't due to a inane mistake on my part this is absolutely insane behavior.

I need to use a variable to make a general script that extracts the children for every node, like so:

get_hierarchy_data <- function(ontology, root_node, outfile){
  parent_offspring_map <- get_correct_offspring_list(ontology)
  for (node in parent_offspring_map$root_node) {
    print(node)
   # actual code omitted
  }
}

get_correct_offspring_list <- function(ontology){
  if (ontology == "CC"){
    return(GOCCOFFSPRING)
  } else if (ontology == "MF") {
    return(GOMFOFFSPRING)
  } else {
    return(GOBPOFFSPRING)
  }
}
r GO.db • 2.1k views
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3
Entering edit mode
8.9 years ago

I guess I'm not sure why you're surprised that this doesn't work, it won't in many languages. You can get around this if you really need to with GOCCCHILDREN[[eval(go)]].

Edit: BTW, you might find this to be informative.

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0
Entering edit mode

I kinda had an inkling that that was the problem, and that I had to evaluate the char-vector at runtime, but I thought it couldn't be, since R is supposedly so high level. I guess I have been spoiled by non-blub languages:

Ended up using pyper which pipes to R through Python:

command_template = 'all_children <- GO{ontology}OFFSPRING$"{node}"'
command = command_template.format(ontology=ontology, node=root_node)
r_session(command)
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0
Entering edit mode
8.8 years ago
library(GO.db)
gmo = as.list(GOMFOFFSPRING)
term = "GO:1903763"

gmo[term]
$`GO:1903763`
[1] "GO:0086020" "GO:0086075" "GO:0086076" "GO:0086077" "GO:0086078"
[6] "GO:0086079"

Must have been some GO.db object strangeness...

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