run_analysis: Run analysis of a batch correction

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

Run analysis of a batch correction

Description

This function only runs under the assumption that the batch correction has been run with the cyCombine workflow in mind. Some result preparation can be necessary, if cyCombine was not used during batch correction. This function assumes that the uncorrected data us stored under the name "{data_dir}/{tool}_{data}{variant}{uncorrected_extension}.RDS" and the corrected data is stored with the name "{data_dir}/{tool}_{data}{variant}{corrected_extension}.RDS". The analysis currently encompass marker-wise density plots, UMAP of corrected vs uncorrected, and Earth Movers Distance.

Usage

run_analysis(
  tool,
  data,
  data_dir,
  uncorrected_extension = "_uncorrected",
  corrected_extension = "_corrected",
  variant = NULL,
  uncorrected_variant = NULL,
  use_cycombine_uncor = FALSE,
  restart = FALSE,
  md = NULL,
  panel = NULL,
  markers = NULL,
  celltype_col = NULL,
  segment = "",
  binSize = 0.1,
  rlen = 10,
  gridsize = 8,
  seed = 473,
  umap_size = 20000
)

Arguments

tool	The name of the tool used to batch correct
data	The name of the data used
data_dir	The location of the uncorrected and corrected data
uncorrected_extension	The extension used to name the uncorrected data. Default: "_uncorrected
corrected_extension	The extension used to name the corrected data. Default: "_corrected"
variant	Optional: A parameter to set a variant name of an experiment
uncorrected_variant	Optional: A parameter to set a variant specific to the uncorrected data
use_cycombine_uncor	If TRUE, the uncorrected data made by cyCombine will be used.
restart	If TRUE, the SOM grid will be calculated even if it has been computed and stored previously
md	Optional: Metadata filename. Currently not useful
panel	Optional: If given, it will be used to define markers. Otherwise the function get_markers will be used
markers	Optional: Manually define markers to use in plots and performance metrics
celltype_col	Optional: If the cell types are known, specify which column they are defined in. If NULL, a clustering will be run.
segment	Optional: Run only a specific segment of the analysis. Options include: "emd", "density", "umap"
binSize	The size of bins to use when binning data
rlen	Number of times the data is presented to the SOM network
gridsize	The gridsize to use when clustering. Only used if no celltype_col is given
seed	The seed to use when creating the UMAP
umap_size	Number of cells to include in UMAP

Examples

## Not run: 
run_analysis(tool = "cycombine",
 data = "dfci1",
 data_dir = "_data")
 run_analysis(tool = "cycombine",
 data = "FR-FCM-ZY34",
 data_dir = "_data",
 variant = "_p3",
 panel = "/attachments/MC_panel3.xlsx")
 
## End(Not run)

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