detect_batch_effect: Full function for detection of batch effects using cluster...

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

Full function for detection of batch effects using cluster proportions

Description

This function is used for batch effect detection in multidimensional datasets. The function applies a SOM-based clustering to a dataset in order to compare not only marker expression differences across batches, but also the cluster percentages in each batch to detect possible populations that are over-/under-represented in a single batch. This is coupled with UMAP plots to assist the interpretation of the results. However, this is primarily meaningful for sets with 3-30 batches - in cases outside this range, only the UMAPs will be generated.

Usage

detect_batch_effect(
  df,
  out_dir,
  downsample = NULL,
  norm_method = "scale",
  xdim = 8,
  ydim = 8,
  seed = 382,
  markers = NULL,
  batch_col = "batch",
  label_col = "label",
  name = "raw data"
)

Arguments

df	Tibble containing the expression data and batch information. See prepare_data.
out_dir	Directory for plot output
downsample	Number of cells to include in detection. If not specified all cells will be used. One should be careful with the downsampling here as too strong downsampling leads to spurious results.
norm_method	Normalization methods (options = 'scale' and 'rank')
xdim	Grid size in x-axis for SOM (default = 8)
ydim	Grid size in y-axis for SOM (default = 8)
seed	Random seed for reproducibility
markers	If only some markers should be used this parameter is used to define them. If not set, all markers are used.
batch_col	Name of column containing batch information
label_col	If existing labels should be used, this column must be present in the data
name	Name of dataset - used for plot titles

See Also

Other detect_batch_effect: detect_batch_effect_express()

Examples

## Not run: 
detect_batch_effect(df = exprs)
detect_batch_effect(df = exprs, xdim = 8, ydim = 8, seed = 382,
                    markers = c('CD3', 'CD4', 'CD8a', 'CD20', 'CD19', 'CD56', 'CD33'))

## End(Not run)

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