calculate_FalseNegative: Calculate False Negative markers for SingleCellExperiment...

In vallotlab/IDclust: Iterative Differential Clustering for single-cell

Calculate False Negative markers for SingleCellExperiment object

Description

Calculate False Negative markers for SingleCellExperiment object

Usage

calculate_FalseNegative(
  object,
  true_marker_list,
  differential_function = differential_ChromSCape,
  by = "IDcluster",
  logFC.th = log2(1.5),
  qval.th = 0.01,
  ...
)

Arguments

object	A SingleCellExperiment object
differential_function	A function that take in entry a SingleCellExperiment object and parameters passed in ... and returns a data.frame containing the significantly differential features for each cluster.
by	A character specifying the name of the metadata column referencing the clusters.
...	Additional parameters passed to the differential_function. See differential_ChromSCape() for more information on additional parameters for the default function.
nThreads	If runFDR==TRUE. An integer specifying of threads to use for the calculation of the FDR.
iterations	An integer specifyung the number of iterations of random subsampling to run.

Examples

if(requireNamespace("ChromSCape", quietly=TRUE)){
data("scExp", package = "IDclust")
scExp = ChromSCape::find_clusters_louvain_scExp(scExp, resolution = 0.1)
FDR_df = calculate_FalseNegative(scExp, nThreads = 1, iterations = 2)
head(FDR_df)
}

vallotlab/IDclust documentation built on Feb. 16, 2023, 8:58 a.m.