prep.lsn.type.matrix: Prepare Lesion Type Matrix

In GRIN2: Genomic Random Interval (GRIN)

Prepare Lesion Type Matrix

Description

The function prepare a lesion matrix with all types of lesions affecting certain gene as a row and each patient as a column.

Usage

prep.lsn.type.matrix(ov.data, min.ngrp = 0)

Arguments

ov.data	list of six data.frames that represent the output results of the find.gene.lsn.overlaps function.
min.ngrp	if specified, rows with number of patients affected by all different types of lesions that's less than the specified number will be discarded (default is 0; will return all genes affected by any type of lesions in at least one patient).

Details

The function returns a lesion matrix with each row as a gene and each column is a patient. If a gene is affected by one type of lesions in a certain patient, the entry will be labelled by lesion type (for example: gain OR mutation). However, if the same gene is affected by more than one type of lesions in a certain patient (for example: gain AND mutation), the entry will be labelled as "multiple". If the gene is not affected by any lesion, the entry for this patient will be labelled as "none".

Value

The function returns a lesion matrix with all types of lesions affecting certain gene as a row and each patient as a column.

Author(s)

Stanley Pounds [e-mail]

References

Pounds, Stan, 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.

See Also

prep.gene.lsn.data(), find.gene.lsn.overlaps()

Examples

data(lesion.data)
data(hg19.gene.annotation)

# prepare gene and lesion data for later computations:
prep.gene.lsn=prep.gene.lsn.data(lesion.data,
                                 hg19.gene.annotation)

# determine lesions that overlap each gene (locus):
gene.lsn.overlap=find.gene.lsn.overlaps(prep.gene.lsn)

# prepare the lesion matrix with a minimum of 5 patients affected by any type of lesion in the
# gene to be included in the final matrix
lsn.type.mtx=prep.lsn.type.matrix(gene.lsn.overlap, min.ngrp=5)

GRIN2 documentation built on April 4, 2025, 1:41 a.m.