view_curated_oagenes {SkeletalVis} | R Documentation |
View curated osteoarthritis associated genes
Description
Retrieves the OATargets table of literature curated genes associated with osteoarthritis joint damage in animals.
Usage
view_curated_oagenes(skeletalvis)
Arguments
skeletalvis |
The path to the SkeletalVis folder. |
Value
A data frame with the following columns:
- PMID
The PubMed ID of the paper describing the observation.
- Gene
The human gene symbol of the gene modulated in the study.
- Effect on gene product
The effect of the gene modulation on the gene product.
- Model
The type of OA model where the gene has been modulated.
- Susceptibility observed
Increase (detrimental) or decrease (protective) in OA severity upon gene modulation.
- Inferred gene effect
Based on the modulation effect, whether the gene is protective or detrimental in OA.
- Delivery
The tissue specificity of the gene modulation.
- Species
The species under study.
- pub_date
The date of publication (epub).
- LastAuthor
The last author of the publication.
- Type
Genetic or exogenous modulation.
- Intervention
For exogenous modulations, the method of gene modulation.
- simpleModel
The broad type of OA model where the gene has been modulated.
- effectConsensus
Consensus inferred gene effect across observations; 'ambiguous' if discrepancies exist.
- NumStudies
The number of publications studying each gene.
Examples
skeletalvis <- load_skeletalvis(demo=TRUE)
oatargets <- view_curated_oagenes(skeletalvis)