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CNVcalling for a List of Seurat Objects Performs Copy Number Variation (CNV) analysis on a list of Seurat objects.

CNVcallingList.Rd

CNVcalling for a List of Seurat Objects Performs Copy Number Variation (CNV) analysis on a list of Seurat objects.

Usage

CNVcallingList(
  seuratList,
  assay = NULL,
  referenceVar = NULL,
  referenceLabel = NULL,
  scaleOnReferenceLabel = TRUE,
  denoise = TRUE,
  thresholdPercentile = 0.01,
  geneMetadata = getGenes(),
  windowSize = 150,
  windowStep = 10,
  saveGenomicWindows = FALSE,
  topNGenes = 7000,
  chrArmsToForce = NULL,
  genesToForce = NULL,
  regionToForce = NULL
)

Arguments

seuratList

A list of Seurat objects containing the data for CNV analysis. Each object can be either single-cell or spatial transcriptomics data.

assay

Name of the assay to run the CNV analysis on. Defaults to the results of prepareCountsForCNVAnalysis if available.

referenceVar

The name of the metadata column in the Seurat object that contains reference annotations.

referenceLabel

The label within referenceVar that specifies the reference population (can be any type of annotation).

scaleOnReferenceLabel

Logical. If TRUE (default), scales the results based on the reference population.

denoise

Logical. If TRUE (default), applies denoising to the data.

thresholdPercentile

Numeric. Specifies the quantile range to consider (e.g., 0.01 keeps values between the 1st and 99th percentiles). Higher values filter out more background noise.

geneMetadata

A dataframe containing gene metadata, typically from Ensembl.

windowSize

Integer. Defines the size of genomic windows for CNV analysis.

windowStep

Integer. Specifies the step size between genomic windows.

saveGenomicWindows

Logical. If TRUE, saves genomic window information in the current directory (default = FALSE).

topNGenes

Integer. The number of top-expressed genes to retain in the analysis.

chrArmsToForce

A chromosome arm (e.g., "8p", "3q") or a list of chromosome arms (e.g., c("3q", "8p", "17p")) to force into the analysis. If specified, all genes within the given chromosome arm(s) will be included.

genesToForce

A list of genes to force into the analysis (e.g. c("FOXP3","MUC16","SAMD15")).

regionToForce

Chromosome region to force into the analysis (vector containing chr, start, end).

Value

A list of Seurat objects, where each:

  • Contains an additional assay with genomic scores per genomic window.

  • Has a new CNV fraction column added to its metadata.