Comments (2)
Dear Elmar Bucher,
Thanks for your appreciation and the feedback of my package!
I checked the genes in the PPI network matrix in several ways but cannot find such duplications:
- I checked the Entrez ID in the matrix with function
duplicated
in R and there is no duplication in both matrices:which(duplicated(rownames(net13Jun12.m)))
, and the result showedinteger(0)
which means none of them are identical. - I also annotated the Enterz ID into Gene Symbol, and then checked the duplications. But there is still no one for
net13Jun12.m
and only three innet17Jan16.m
, which is much less than what you observed. - And I checked the matrices you provided, it seems those genes which are excluded do not show up in the reshaped ones.
So I am wondering how you actually identify such duplications, could you provide more details so that I can help you further?
Best,
Weiyan
from landscent.
Dear Weiyan,
I see what went wrong. I am sorry for that.
I am not really an R programmer. So I downloaded the network to a tab separated file like this.
library(LandSCENT)
data(net13Jun12.m)
write.table(net13Jun12.m, "net13Jun2012.original.entrez.m.tsv", sep="\t")
And uploaded it into Python3 for mapping the entrenz gene identifier to other gene identifiers.
import pandas as pd
df_net13 = pd.read_csv("net13Jun2012.original.entrez.m.tsv", sep="\t")
Because gene identifier not always map one to one, I used the pandas command:
df_net13 = df_net13.drop_duplicates()
Now drop_duplicates removes all duplicate row, but it ignores the index.
So it removed genes that are in the network the same way connected then already another gene.
I am sorry about that!
I think I can close this issue.
Elmar
from landscent.
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