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danro9685 / OncoScore

OncoScore is a tool to measure the association of genes to cancer based on citation frequency in biomedical literature. The manuscript of the method is published on Scientific Reports and available at http://www.nature.com/articles/srep46290.
https://danro9685.github.io/OncoScore/
GNU General Public License v3.0
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Error - genes with no literature data #10

Closed sigven closed 8 years ago

sigven commented 8 years ago

Hi,

I have just tried your software (v 1.0.0) in order to build a ranking of genes based on cancer relevance. During test runs, I experience that OncoScore::perform.query fail/crash if any gene in my submission list have no hits in PubMed (e.g. the gene TBC1D3C) Here is the error message that appears:

Error in if ((is.na(s1) || is.na(s2)) && (get.count.of.list(webget) == : missing value where TRUE/FALSE needed In addition: Warning messages:

Sigve

luca-dex commented 8 years ago

I can't reproduce the issue:

> perform.query('TBC1D3C')
### Starting the queries for the selected genes.

### Performing queries for cancer literature 
    Number of papers found in PubMed for TBC1D3C was: -1 

### Performing queries for all the literature 
    Number of papers found in PubMed for TBC1D3C was: -1 
        CitationsGene CitationsGeneInCancer
TBC1D3C            -1                    -1
Warning messages:
1: In perform.query(c("TBC1D3C")) : TBC1D3C not found on PubMed

2: In perform.query(c("TBC1D3C")) : TBC1D3C not found on PubMed
sigven commented 8 years ago

Hi,

You are right. I do not see the error any longer (for whatever reason). You can close the issue.

luca-dex commented 8 years ago

:)