sce2FCS: Convert SingelCellExperiment into flowSet and store as FCS...

In biosurf/cyCombine: Robust integration of single-cell cytometry datasets within and across technologies

Convert SingelCellExperiment into flowSet and store as FCS files

Description

Wrapper function that makes it easier to go from a SCE to flowSet and written FCS files. The function uses CATALYST::sce2fcs and flowCore::write.flowSet to store the FCS files.

Usage

sce2FCS(
  sce,
  outdir = NULL,
  split_by = "sample_id",
  assay = "counts",
  keep_dr = TRUE,
  keep_cd = TRUE,
  randomize = FALSE
)

Arguments

sce	SingleCellExperiment to write to FCS files
outdir	If given, the flowSet will be stored in FCS files
split_by	NULL or a character string specifying a colData(x) column to split by.
assay	a character string specifying which assay data to use; valid values are assayNames(x). When writing out FCS files, this should correspond to count-like data!
keep_cd, keep_dr	logials specifying whether cell metadata (stored in colData(x)) and dimension reductions (stored in reducedDims(x)), respectively, should be kept or dropped.
randomize	(Default: FALSE) Logical determining whether counts are randomized for plotting purposes or not. Only works when assay = "counts" (default).

See Also

Other export: df2SCE()

Examples

## Not run: 
 sce2FCS(sce, outdir = "fcs_files")
  
## End(Not run)

biosurf/cyCombine documentation built on May 23, 2024, 4:07 a.m.