This function orders and indexes lesion data by lesion type, chromosome, and subject ID. It prepares lesion data for downstream GRIN analysis by structuring it in a way that facilitates efficient access and overlap computations.
order.index.lsn.data(lsn.data)A list with two elements:
The input lesion data, ordered by lesion type, chromosome, and subject.
A data.frame with two columns, row.start and row.end, indicating the index range of lesions for each subject-lesion type-chromosome combination. For example, if a patient has a single deletion on chromosome 5, row.start will equal row.end. If there are four deletions, the range will span four rows.
A data.frame containing lesion data formatted for GRIN. It must include the following five columns:
Patient identifier.
Chromosome on which the lesion is located.
Start position of the lesion.
End position of the lesion.
Lesion type (e.g., gain, loss, mutation, fusion, etc...).
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and 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.
data(lesion_data)
ordered.lsn <- order.index.lsn.data(lesion_data)
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