FRmatch: FR-Match for single cell RNA-seq data

In JCVenterInstitute/FRmatch: Cell type matching in single-cell RNA-sequencing data using FR-Match

FR-Match for single cell RNA-seq data

Description

This is a user-end wrapper function that implements the steps of cell type matching between two single cell RNA-seq experiments (namely, query and reference) using the cluster-to-cluster FR-Match approach.

Usage

FRmatch(
  sce.query,
  sce.ref,
  use.cosine = TRUE,
  filter.size = 5,
  filter.fscore = NULL,
  filter.nomarker = FALSE,
  add.pseudo.marker = FALSE,
  pseudo.expr = 1,
  subsamp.size = 20,
  subsamp.iter = 1000,
  subsamp.seed = 1,
  numCores = NULL,
  prefix = c("query.", "ref."),
  verbose = 1,
  return.all = FALSE,
  ...
)

Arguments

sce.query	Data object of the SingleCellExperiment class for query experiment. See details in sce.example.
sce.ref	Data object of the SingleCellExperiment class for reference experiment. See details in sce.example.
filter.size, filter.fscore, filter.nomarker	Filtering out small/poor-quality/no-marker clusters. Default: filter.size=5, filter based on the number of cells per cluster; filter.fscore=NULL, do not filter based on the F-beta score, otherwise specify a numeric value between 0 and 1; filter.nomarker=FALSE, filter based on the boolean variable indicating if to filter reference clusters with no marker genes available in query.
add.pseudo.marker, pseudo.expr	Adding pseudo marker to stabilize no expression clusters in the marker gene feature space. Default: add.pseudo.marker=FALSE, boolean. Pseudo marker expression values are drawn from uniform distribution from 0 to pseudo.expr. Default: pseudo.expr=1, numeric, for the min-max scaled data after normalization.
subsamp.size, subsamp.iter, subsamp.seed	Numeric variables for iterative subsampling size, number of iterations, and random seed for iterations. YMMV.
numCores	Number of cores for parallel computing. Default: NULL, use the maximum number of cores detected by detectCores. Otherwise, specify by an integer value.
prefix	Prefix names for query and reference clusters. Default: prefix=c("query.", "ref.").
verbose	Numeric value indicating levels of details to be printed. Default: 1, only print major steps. If 0, no verbose; if 2, print all, including warnings.
return.all	Boolean variable indicating if to return all results (such as runs, etc.). Default: FALSE.
...	Additional arguments passed to FRtest, including use.cosine.

Value

A list of:

settings	Record of customized parameter settings specified in the function.
pmat	A matrix of p-values. Rows are reference clusters, and columns are query clusters.
statmat	A matrix of FR statistics. Rows are reference clusters, and columns are query clusters.

If return.all = TRUE, more intermediate results are returned.

See Also

Visualization of matching results using plot_FRmatch, plot_bi_FRmatch.

Examples

## Not run: 
data("sce.example")
FRmatch(sce.example, sce.example)

## End(Not run)

JCVenterInstitute/FRmatch documentation built on June 11, 2025, 12:28 a.m.