annotation_issues: Check for genomic annotation problems in IS matrices.

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Check for genomic annotation problems in IS matrices.

Description

This helper function checks if each individual integration site, identified by the mandatory_IS_vars(), has been annotated with two or more distinct gene symbols.

Usage

annotation_issues(matrix)

Arguments

matrix

Either a single matrix or a list of matrices, ideally obtained via import_parallel_Vispa2Matrices() or import_single_Vispa2Matrix()

Value

Either NULL if no issues were detected or 1 or more data frames with genomic coordinates of the IS and the number of distinct genes associated

See Also

Other Import functions helpers: date_formats(), default_af_transform(), default_iss_file_prefixes(), matching_options(), quantification_types()

Examples

data("integration_matrices", package = "ISAnalytics")
annotation_issues(integration_matrices)

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.