Question: kegg orthology entry to pathway ko
1
gravatar for luyang1005
16 months ago by
luyang100510
luyang100510 wrote:

Hi, community,

I have used EggNOG produce a table(as shown below) which contains the kegg orthlogy entry. May I know how to get the pathway name based on the list column? 

Thanks in advance.

query list
k119_1151408_63 K00864
k119_1151408_78 K13963
k119_1151433_12 K00873

 

kegg • 247 views
ADD COMMENTlink modified 16 months ago by James W. MacDonald51k • written 16 months ago by luyang100510
Answer: kegg orthology entry to pathway ko
0
gravatar for James W. MacDonald
16 months ago by
United States
James W. MacDonald51k wrote:

You could use the KEGGREST package:

> library(KEGGREST)

> keggLink("pathway", c("K00864","K13963","K00873"))
      ko:K00864       ko:K00864       ko:K00864       ko:K00864       ko:K00864
"path:map00561"  "path:ko00561" "path:map01100"  "path:ko01100" "path:map03320"
      ko:K00864       ko:K00864       ko:K00864       ko:K13963       ko:K13963
 "path:ko03320" "path:map04626"  "path:ko04626" "path:map05146"  "path:ko05146"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map00010"  "path:ko00010" "path:map00230"  "path:ko00230" "path:map00620"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
 "path:ko00620" "path:map01100"  "path:ko01100" "path:map01110"  "path:ko01110"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map01120"  "path:ko01120" "path:map01130"  "path:ko01130" "path:map01200"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
 "path:ko01200" "path:map01230"  "path:ko01230" "path:map04922"  "path:ko04922"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map04930"  "path:ko04930" "path:map05165"  "path:ko05165" "path:map05203"
      ko:K00873       ko:K00873       ko:K00873
 "path:ko05203" "path:map05230"  "path:ko05230"

Or maybe a bit clearer:

> z <- keggLink("pathway", c("K00864","K13963","K00873"))

> lapply(split(z, names(z)), unique)
$`ko:K00864`
[1] "path:map00561" "path:ko00561"  "path:map01100" "path:ko01100"
[5] "path:map03320" "path:ko03320"  "path:map04626" "path:ko04626"

$`ko:K00873`
 [1] "path:map00010" "path:ko00010"  "path:map00230" "path:ko00230"
 [5] "path:map00620" "path:ko00620"  "path:map01100" "path:ko01100"
 [9] "path:map01110" "path:ko01110"  "path:map01120" "path:ko01120"
[13] "path:map01130" "path:ko01130"  "path:map01200" "path:ko01200"
[17] "path:map01230" "path:ko01230"  "path:map04922" "path:ko04922"
[21] "path:map04930" "path:ko04930"  "path:map05165" "path:ko05165"
[25] "path:map05203" "path:ko05203"  "path:map05230" "path:ko05230"

$`ko:K13963`
[1] "path:map05146" "path:ko05146"
ADD COMMENTlink written 16 months ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 402 users visited in the last hour