Entering edit mode
Qian Liu
▴
110
@qian-liu-4216
Last seen 10.2 years ago
Hi there,
I need some help with the RpsiXML.
Question1:I have about 200 genes on the list, is it possible to pull
out
protein-protein interaction in one step or into one XML file?
Question2: I use FOR Loop to pull out the protein-protein interaction
data
for each gene.
I have list of genes. The 3rd gene "DRD1" dosen't have output from
IntAct.
the function parsePsimi25Interaction will show the following error
message
R code:
genelist=c("HTR7","FRG1","DRD1","BRCA2")
n=length(genelist)
for (k in 1:n){
url254L=paste("
http://www.ebi.ac.uk/intact/export?query=q%3Dspecies%253Ahuman%2BAND%2
B",genelist[k
],
"%26sort%3Drigid%2Basc%26rows%3D30%26start%3D0%26facet%3Dtrue%26facet.
missing%3Dtrue%26facet.field%3Dexpansion%26facet.field%3DinteractorTyp
e_id&format=xml_2_54&conversationContext=1",sep='')
intactSample=parsePsimi25Interaction(url254L,INTACT.PSIMI25,verbose=FA
LSE)
........
}
The first two genes works fine, but 3rd one show the following error
message,and program stopped.
I try to add if statement like is.na, NULL, exists, but none of them
can
test whether the URL leads to real output.
So what statement should I use so that the program can move on?
Thank you,
Qian
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
25% ==========>
50% ====================>
75% ==============================>
100% ========================================>
Parsing interactions:
..
1 Entries found
Parsing entry 1
Parsing experiments: ...
Parsing interactors:
17% =======>
33% =============>
50% ====================>
67% ===========================>
83% =================================>
100% ========================================>
Parsing interactions:
...
EntityRef: expecting ';'
EntityRef: expecting ';'
EntityRef: expecting ';'
EntityRef: expecting ';'
EntityRef: expecting ';'
EntityRef: expecting ';'
EntityRef: expecting ';'
Error: 1: EntityRef: expecting ';'
2: EntityRef: expecting ';'
3: EntityRef: expecting ';'
4: EntityRef: expecting ';'
5: EntityRef: expecting ';'
6: EntityRef: expecting ';'
7: EntityRef: expecting ';'
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