giLikelihood: Genomic instability likelihood

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

Genomic instability likelihood

Description

This function computes the genomic instability likelihood

Usage

giLikelihood(
  inferCNV,
  recompute = TRUE,
  distros = c(1, 3),
  tumor = NULL,
  normal = NULL
)

Arguments

inferCNV	InferCNV-class object
recompute	Logical, whether the model fits should be re-computed
distros	Vector of 2 integers indicating the minimum and maximum number of Gaussian models to fit
tumor	Optional vector of integers indicating the Gaussians considered as tumors
normal	Optional vector of integers indicating the Gaussians considered as normal. This is only useful when no null model has been provided for the analysis

Value

Updated inferCNV-class object with gi_likelihood slot

See Also

[genomicInstabilityScore()] to estimate the genomic instability score for each cell in the dataset, and [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)$TPM
set.seed(1)
tpm_matrix <- tpm_matrix[, sample(ncol(tpm_matrix), 500)]
cnv <- inferCNV(tpm_matrix)
cnv <- genomicInstabilityScore(cnv)
cnv <- giLikelihood(cnv, distros=c(3, 3), tumor=2:3)
print(cnv$gi_fit)
plot(density(cnv$gi_likelihood, from=0, to=1))

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