warning_filter_correlated_cell_scExp: warning_filter_correlated_cell_scExp

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

warning_filter_correlated_cell_scExp

Description

warning_filter_correlated_cell_scExp

Usage

warning_filter_correlated_cell_scExp(
  scExp,
  random_iter,
  corr_threshold,
  percent_correlation,
  run_tsne,
  downsample,
  verbose
)

Arguments

scExp	A SingleCellExperiment object containing 'Cor', a correlation matrix, in reducedDims.
random_iter	Number of random matrices to create to calculate random correlation scores. (50)
corr_threshold	Quantile of random correlation score above which a cell is considered to be 'correlated' with another cell. (99)
percent_correlation	Percentage of the cells that any cell must be 'correlated' to in order to not be filtered. (1)
run_tsne	Re-run tsne ? (FALSE)
downsample	Number of cells to calculate correlation filtering threshold ? (2500)
verbose	(TRUE)

Value

Warnings or Errors if the input are not correct

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.