get_residuals: Return Pearson or deviance residuals of regularized models

In sctransform: Variance Stabilizing Transformations for Single Cell UMI Data

Return Pearson or deviance residuals of regularized models

Description

Return Pearson or deviance residuals of regularized models

Usage

get_residuals(
  vst_out,
  umi,
  residual_type = "pearson",
  res_clip_range = c(-sqrt(ncol(umi)), sqrt(ncol(umi))),
  min_variance = vst_out$arguments$min_variance,
  cell_attr = vst_out$cell_attr,
  bin_size = 256,
  verbosity = vst_out$arguments$verbosity,
  verbose = NULL,
  show_progress = NULL
)

Arguments

vst_out	The output of a vst run
umi	The UMI count matrix that will be used
residual_type	What type of residuals to return; can be 'pearson' or 'deviance'; default is 'pearson'
res_clip_range	Numeric of length two specifying the min and max values the results will be clipped to; default is c(-sqrt(ncol(umi)), sqrt(ncol(umi)))
min_variance	Lower bound for the estimated variance for any gene in any cell when calculating pearson residual; default is vst_out$arguments$min_variance
cell_attr	Data frame of cell meta data
bin_size	Number of genes to put in each bin (to show progress)
verbosity	An integer specifying whether to show only messages (1), messages and progress bars (2) or nothing (0) while the function is running; default is 2
verbose	Deprecated; use verbosity instead
show_progress	Deprecated; use verbosity instead

Value

A matrix of residuals

Examples

vst_out <- vst(pbmc, return_cell_attr = TRUE)
pearson_res <- get_residuals(vst_out, pbmc)
deviance_res <- get_residuals(vst_out, pbmc, residual_type = 'deviance')

sctransform documentation built on Oct. 19, 2023, 9:08 a.m.