Re: [R] Why I can't retrieve GO identifier correctly?
[EMAIL PROTECTED] wrote:
Hello, R experts,
I tried to retrieve all biological process GO terms at level 3 starting
biological process as level 1 using the code as bellows:
1 library(GO)
2 library(GOstats)
3 level2-getGOChildren(GO:0008150)$GO:0008150$Children
4 for ( i in 1:length(level2)) {
5level3 - getGOChildren(level2[i])$level2[i]$Children
If you want to index by an object that contains a character (or string),
you have to use [[]] rather than $.
The question is completely independent of GO, so don't confuse potential
responders who expect you to send messages re. Bioconductor packages to
the corresponding list.
Uwe Ligges
6for ( j in 1:length(level3)){
7 level3term - getGOTerm(as.character(level3[j]))$BP$level3[j]
8 level3term
9}
10 }
What is the difference between line 3 and line5? In the line 3 I retrieved the
GO identifiers at level 2 successfullly but in the line 5 I got nothing. How to
correct the line 5 to retrieve the GO terms at level 3 correctly?
Thank you in advance!
Josh
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Re: [R] Why I can't retrieve GO identifier correctly?
Hello, Uwe and Robert,
Thank you for your help! I fixed the problem as your suggestion. I run into a
new issue: I can't sink the output to a file in the script within loops as
bellows, but I can sink it in the command line( I run R1.9.1 on WinXP).
The scrip:
sink(C:/level3BPterm.txt)
level2-getGOChildren(GO:0008150)$GO:0008150$Children
for ( i in 1:length(level2)) {
level3 - c(getGOChildren(level2[i])[[1]]$Children)
for ( j in 1:length(level3)){
level3term - getGOTerm(as.character(level3[j]))$BP
paste(level3term)
}
}
sink()
Run in the command line:
sink(C:/level3BPterm.txt)
paste(level3term)
sink()
So what is wrong with my script?
Thanks again
Josh
Quoting Uwe Ligges [EMAIL PROTECTED]:
[EMAIL PROTECTED] wrote:
Hello, R experts,
I tried to retrieve all biological process GO terms at level 3 starting
biological process as level 1 using the code as bellows:
1 library(GO)
2 library(GOstats)
3 level2-getGOChildren(GO:0008150)$GO:0008150$Children
4 for ( i in 1:length(level2)) {
5level3 - getGOChildren(level2[i])$level2[i]$Children
If you want to index by an object that contains a character (or string),
you have to use [[]] rather than $.
The question is completely independent of GO, so don't confuse potential
responders who expect you to send messages re. Bioconductor packages to
the corresponding list.
Uwe Ligges
6for ( j in 1:length(level3)){
7 level3term - getGOTerm(as.character(level3[j]))$BP$level3[j]
8 level3term
9}
10 }
What is the difference between line 3 and line5? In the line 3 I retrieved
the
GO identifiers at level 2 successfullly but in the line 5 I got nothing.
How to
correct the line 5 to retrieve the GO terms at level 3 correctly?
Thank you in advance!
Josh
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
[EMAIL PROTECTED] mailing list
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Re: [R] Why I can't retrieve GO identifier correctly?
[EMAIL PROTECTED] wrote:
Hello, Uwe and Robert,
Well, you are sending your message to Uwe and R-help rather than Uwe
and Robert ..
Thank you for your help! I fixed the problem as your suggestion. I run into a
new issue: I can't sink the output to a file in the script within loops as
bellows, but I can sink it in the command line( I run R1.9.1 on WinXP).
The scrip:
sink(C:/level3BPterm.txt)
level2-getGOChildren(GO:0008150)$GO:0008150$Children
for ( i in 1:length(level2)) {
level3 - c(getGOChildren(level2[i])[[1]]$Children)
for ( j in 1:length(level3)){
level3term - getGOTerm(as.character(level3[j]))$BP
paste(level3term)
You need to print() it! But you really want to return() it from a
function ...
Uwe
}
}
sink()
Run in the command line:
sink(C:/level3BPterm.txt)
paste(level3term)
sink()
So what is wrong with my script?
Thanks again
Josh
Quoting Uwe Ligges [EMAIL PROTECTED]:
[EMAIL PROTECTED] wrote:
Hello, R experts,
I tried to retrieve all biological process GO terms at level 3 starting
biological process as level 1 using the code as bellows:
1 library(GO)
2 library(GOstats)
3 level2-getGOChildren(GO:0008150)$GO:0008150$Children
4 for ( i in 1:length(level2)) {
5level3 - getGOChildren(level2[i])$level2[i]$Children
If you want to index by an object that contains a character (or string),
you have to use [[]] rather than $.
The question is completely independent of GO, so don't confuse potential
responders who expect you to send messages re. Bioconductor packages to
the corresponding list.
Uwe Ligges
6for ( j in 1:length(level3)){
7 level3term - getGOTerm(as.character(level3[j]))$BP$level3[j]
8 level3term
9}
10 }
What is the difference between line 3 and line5? In the line 3 I retrieved
the
GO identifiers at level 2 successfullly but in the line 5 I got nothing.
How to
correct the line 5 to retrieve the GO terms at level 3 correctly?
Thank you in advance!
Josh
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Why I can't retrieve GO identifier correctly?
[EMAIL PROTECTED] writes:
Hello, R experts,
I tried to retrieve all biological process GO terms at level 3 starting
biological process as level 1 using the code as bellows:
1 library(GO)
2 library(GOstats)
3 level2-getGOChildren(GO:0008150)$GO:0008150$Children
4 for ( i in 1:length(level2)) {
5level3 - getGOChildren(level2[i])$level2[i]$Children
6for ( j in 1:length(level3)){
7 level3term - getGOTerm(as.character(level3[j]))$BP$level3[j]
8 level3term
9}
10 }
What is the difference between line 3 and line5? In the line 3 I retrieved the
GO identifiers at level 2 successfullly but in the line 5 I got nothing. How to
correct the line 5 to retrieve the GO terms at level 3 correctly?
Thank you in advance!
Josh
I think you'll have better luck with that question if you take it to
the Bioconductor list.
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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