salvage_problematic: Salvaging problematic channels - one at a time

In shdam/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,
  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
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)

shdam/cyCombine documentation built on June 12, 2022, 11:29 p.m.