batch_correct: Run batch correction on data

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

Run batch correction on data

Description

This is a wrapper function for the cyCombine batch correction workflow. To run the workflow manually, type "batch_correct" to see the source code of this wrapper and follow along or read the vignettes on the GitHub page https://github.com/biosurf/cyCombine.

Usage

batch_correct(
  df,
  label = NULL,
  xdim = 8,
  ydim = 8,
  rlen = 10,
  parametric = TRUE,
  method = c("ComBat", "ComBat_seq"),
  ref.batch = NULL,
  seed = 473,
  covar = NULL,
  anchor = NULL,
  markers = NULL,
  norm_method = "scale",
  ties.method = "average",
  ...
)

Arguments

df	tibble with expression values
label	The cluster or cell type label. Either as a column name or vector.
xdim	The x-dimension size of the SOM.
ydim	The y-dimension size of the SOM.
rlen	Number of times the data is presented to the SOM network
parametric	Default: TRUE. If TRUE, the parametric version of ComBat is used. If FALSE, the non-parametric version is used.
method	Default: "ComBat". Choose "ComBat" for cytometry data and "ComBat_seq" for bulk RNAseq data.
ref.batch	Optional. A string of the batch that should be used as the reference for batch adjustments.
seed	The seed to use when creating the SOM.
covar	The covariate ComBat should use. Can be a vector or a column name in the input tibble. If NULL, no covar will be used
anchor	Experimental: A column or vector specifying which samples are replicates and which are not. If specified, this column will be used as a covariate in ComBat. Be aware that it may be confounded with the condition.
markers	Markers to normalize. If NULL, markers will be found using the get_markers function.
norm_method	Normalization method. Should be either 'rank', 'scale' or 'qnorm'. Default: 'scale'
ties.method	The method to handle ties, when using rank. Default: 'average'. See ?rank for other options.
...	Additional parameters to pass onto ComBat and ComBat_seq

See Also

Other batch: correct_data(), create_som(), normalize(), quantile_norm()

Examples

## Not run: 
corrected <- uncorrected %>%
  batch_correct(markers = markers,
  covar = "condition")
  
## End(Not run)

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