GRASP2 truncated phenotype descriptions
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@gokceneraslan-8533
Last seen 4.7 years ago
Germany

Hi,

I am running into truncated phenotype categories when I use GRASP2 like this:

> library(grasp2db)
> GRASP2() %>% tbl(., 'study') %>% filter(PaperPhenotypeDescription %like% '%cystic fibrosis%') %>% select(PaperPhenotypeDescription) %>% as.data.frame
            PaperPhenotypeDescription
1    Cystic fibrosis, lung disease in
2        Cystic fibrosis, severity of
3 Cystic fibrosis with meconium ileus
4         Diabetes in cystic fibrosis

 

Although cystic fibrosis-related categories in GRASP web page are listed as:

 

- Cross-sectional lung function
- Cystic fibrosis lung disease severity
- Cystic fibrosis-related diabetes
- Cystic fibrosis-related diabetes in patients homozygous for F508del CFTR
- Longitudinal lung function
- Lung disease severity
- Meconium ileus in cystic fibrosis
- Meconium ileus in cystic fibrosis (female)  
- Meconium ileus in cystic fibrosis (male)
 

So, my question is why are the categories truncated and why don't they match to the categories on the GRASP web page?

 

grasp2 grasp2db annotationhub • 674 views
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Entering edit mode
@martin-morgan-1513
Last seen 8 days ago
United States

The data in grasp2db are processed as described in the vignette. I looked at the original data source (a tab-delimited text file) and it contains the strings as presented by the grasp2db package; I do not know the processing steps used to create the web interface.

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