count.hits | R Documentation |
Computes the number of genomic lesions ("hits") affecting each gene by lesion category. It also calculates the number of unique subjects whose lesions overlap each gene by lesion type.
count.hits(ov.data)
ov.data |
A list of six |
This function summarizes the output of find.gene.lsn.overlaps()
by generating two key matrices:
nsubj.mtx: For each gene, the number of unique subjects with at least one overlapping lesion of each type.
nhit.mtx: For each gene, the total number of overlapping lesions (hits), regardless of subject redundancy, categorized by lesion type.
For example, if the gene NOTCH1 is affected by three separate mutations in the same subject, that subject will be counted once in nsubj.mtx
, but all three hits will be counted in nhit.mtx
.
A list containing the following components:
lsn.data |
Original input lesion data. |
lsn.index |
A |
gene.data |
Original input gene annotation data. |
gene.index |
A |
nhit.mtx |
A |
nsubj.mtx |
A |
gene.lsn.data |
A |
glp.data |
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
, find.gene.lsn.overlaps
data(lesion_data)
data(hg38_gene_annotation)
# Prepare gene and lesion data for GRIN analysis:
prep.gene.lsn <- prep.gene.lsn.data(lesion_data, hg38_gene_annotation)
# Identify overlapping gene-lesion events:
gene.lsn.overlap <- find.gene.lsn.overlaps(prep.gene.lsn)
# Count the number of subjects and lesions (hits) affecting each gene:
count.nsubj.nhits <- count.hits(gene.lsn.overlap)
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