View source: R/find.gene.lsn.overlaps.R
find.gene.lsn.overlaps | R Documentation |
Identifies overlaps between genes and genomic lesions using the output from the prep.gene.lsn.data()
function.
This function detects all instances where a lesion spans or intersects the genomic coordinates of a gene.
find.gene.lsn.overlaps(gl.data)
gl.data |
A list of five |
A list containing the following components:
lsn.data |
Original input lesion data. |
gene.data |
Original input gene annotation data. |
gene.lsn.data |
A |
gene.lsn.hits |
A |
gene.index |
A |
lsn.index |
A |
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org, Stanley Pounds stanley.pounds@stjude.org
Pounds, S. et al. (2013). A genomic random interval model for statistical analysis of genomic lesion data.
Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.
prep.gene.lsn.data
data(lesion_data)
data(hg38_gene_annotation)
# Prepare gene and lesion data for GRIN-based computations:
prep.gene.lsn <- prep.gene.lsn.data(lesion_data, hg38_gene_annotation)
# Identify genes that are overlapped by lesions:
gene.lsn.overlap <- find.gene.lsn.overlaps(prep.gene.lsn)
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