genomicInstabilityScore: Genomic Instability Analysis

In reef103/genomicInstability: Genomic Instability estimation for scRNA-Seq

Genomic Instability Analysis

Description

This function computes the genomic instability for an object of class inferCNV

Usage

genomicInstabilityScore(cnv, likelihood = FALSE)

Arguments

cnv	Object of class inferCNV generated by inferCNV() function
likelihood	Logical, whether the genomic instability likelihood should be estimated

Value

Object of class inferCNV with updated slots for gis and gisnull

See Also

[inferCNV()] to infer the enrichment of loci-blocks in the gene expression data.

Examples

eh <- ExperimentHub::ExperimentHub()
dset <- eh[["EH5419"]]
tpm_matrix <- SummarizedExperiment::assays(dset)$TPM
set.seed(1)
tpm_matrix <- tpm_matrix[, sample(ncol(tpm_matrix), 500)]
cnv <- inferCNV(tpm_matrix)
cnv <- genomicInstabilityScore(cnv)
plot(density(cnv$gis))

reef103/genomicInstability documentation built on Oct. 10, 2022, 12:33 a.m.