salvage_problematic: Salvaging problematic channels - one at a time

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

Salvaging problematic channels - one at a time

Description

This function imputes the expression values for a single channel based on the information in the other channels. The purpose is to be able to salvage a misstained channel in single batches of an experiment

Usage

salvage_problematic(
  df,
  correct_batches,
  channel,
  label = NULL,
  sample_size = NULL,
  exclude = NULL,
  xdim = 8,
  ydim = 8,
  seed = 482
)

Arguments

df	Dataframe with expression values
correct_batches	Batches with misstaining (or other problem) for which to perform the imputation of 'channel'
channel	Channel (marker) to impute
label	(Optional) Column with group labels to base imputations on
sample_size	Number of cells to base imputation on - defaults to all cells in df not in 'correct_batches'
exclude	Channels to exclude (e.g. other misstained channels not to be used for imputation)
xdim	The x-dimension size of the SOM.
ydim	The y-dimension size of the SOM.
seed	The seed to use when creating the SOM.

See Also

Other merging: impute_across_panels()

Examples

## Not run: 
df_fixed <- df %>%
  salvage_problematic(correct_batches = 1, channel = 'CD127')
  
## End(Not run)

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