Skip to contents

Find disease-associated SNPs occurring at DE-miRNA loci

Source: R/association.R
findMirnaSNPs.Rd

This function allows to identify disease-associated genomic variants affecting differentially expressed miRNA genes or their host genes. To do so, this function uses gwasrapidd to retrieve SNPs-disease associations, and then retains only SNPs that affect DE-miRNA genes or their relative host genes (for intronic miRNAs).

Usage

findMirnaSNPs(mirnaObj, diseaseEFO)

Arguments

mirnaObj

A MirnaExperiment object containing miRNA and gene data

diseaseEFO

The EFO identifier of a disease of interest. This can be identified with the searchDisease() function

Value

A data.frame containing details about disease-SNPs and the associated differentially expressed miRNAs:

  • variant contains SNP identifiers;

  • gene defines the gene affected by a disease-SNP (it may be the miRNA gene itself or the host gene of an intronic miRNA);

  • miRNA.gene specifies the DE-miRNA gene present;

  • miRNA.precursor specifies the name of the miRNA precursor affected by disease-SNPs;

  • chr indicates the chromosome of SNPs;

  • position shows the SNP position;

  • allele displays possible alleles for this SNPs;

  • distance specifies the distance between SNPs and miRNAs;

  • is_upstream indicates whether SNP is upstream of miRNA gene;

  • is_downstream indicates whether SNP is downstream of miRNA gene;

  • mirnaStrand shows the strand;

  • mirnaStartPosition displays the start position of DE-miRNA gene;

  • mirnaEndPosition displays the end position of DE-miRNA gene.

Details

SNPs occurring within miRNAs may have important effects on the biological function of these transcripts. Indeed, a SNP present within a miRNA gene might alter its expression or the spectrum of miRNA targets.

To retrieve disease-SNPs, this function uses gwasrapidd package, which directly queries the NHGRI-EBI Catalog of published genome-wide association studies. After running this function, the user can use the mirVariantPlot() function to produce a trackplot for visualizing the genomic location of SNPs within miRNA genes.

Note

To retrieve disease-associated SNPs, this function makes use of the gwasrapidd package.

References

Ramiro Magno, Ana-Teresa Maia, gwasrapidd: an R package to query, download and wrangle GWAS catalog data, Bioinformatics, Volume 36, Issue 2, January 2020, Pages 649–650, https://doi.org/10.1093/bioinformatics/btz605

Author

Jacopo Ronchi, jacopo.ronchi@unimib.it

Examples

# load example MirnaExperiment object
obj <- loadExamples()

# \donttest{
# search disease
searchDisease("response to antidepressant")
#> Checking for cached EFO traits...
#> Reading EFO traits from cache...
#> Searching for disease: response to antidepressant
#> [1] "response to antidepressant" "response to anticonvulsant"
disId <- "response to antidepressant"

# retrieve associated SNPs
association <- findMirnaSNPs(obj, disId)
#> Querying GWAS Catalog, this may take some time...
#> Finding genomic information of differentially expressed miRNAs...
#> Ensembl site unresponsive, trying asia mirror
#> Ensembl site unresponsive, trying asia mirror
#> After the analysis, 1 variants associated with response to antidepressant were found within differentially expressed miRNA genes
# }