inferCNV: Inference of CNV from expression data

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

Inference of CNV from expression data

Description

This function estimates the CNV score based on expression data

Usage

inferCNV(
  expmat,
  nullmat = NULL,
  species = c("human", "mouse"),
  k = 100,
  skip = 25,
  min_geneset = 10,
  verbose = TRUE
)

Arguments

expmat	Matrix of gene expression profiles or signatures with genes '(entrezID) in rows and samples in columns
nullmat	Optional matrix with same number of rows as expmat to be used as null model
species	Character string indicating the species, either human or mouse
k	Integer indicating the number of genes per set
skip	Interger indicating the displacement of the window for selecting the k genes
min_geneset	Integer indicating the minimum size for the genesets
verbose	Logical, whether progress should be reported

Value

Object of class inferCNV, which is a list containing matrix of nes, and parameters (param), including species, window (k) and skip

Examples

eh <- ExperimentHub::ExperimentHub()
dset <- eh[["EH5419"]]
tpm_matrix <- SummarizedExperiment::assays(dset)$TPM
set.seed(1)
tpm_matrix <- tpm_matrix[, sample(ncol(tpm_matrix), 500)]
cnv <- inferCNV(tpm_matrix)
class(cnv)
names(cnv)
cnv$nes[1:5, 1:3]

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