compare_expression: Compare gene expression between two groups

Description

Compare gene expression between two groups

Usage

compare_expression(
  x,
  umi,
  group,
  val1,
  val2,
  method = "LRT",
  bin_size = 256,
  cell_attr = x$cell_attr,
  y = x$y,
  min_cells = 5,
  weighted = TRUE,
  randomize = FALSE,
  verbosity = 2,
  verbose = NULL,
  show_progress = NULL
)

Value

Data frame of results

Arguments

x: A list that provides model parameters and optionally meta data; use output of vst function
umi: A matrix of UMI counts with genes as rows and cells as columns
group: A vector indicating the groups
val1: A vector indicating the values of the group vector to treat as group 1
val2: A vector indicating the values of the group vector to treat as group 2
method: Either 'LRT' for likelihood ratio test, or 't_test' for t-test
bin_size: Number of genes that are processed between updates of progress bar
cell_attr: Data frame of cell meta data
y: Only used if methtod = 't_test', this is the residual matrix; default is x$y
min_cells: A gene has to be detected in at least this many cells in at least one of the groups being compared to be tested
weighted: Balance the groups by using the appropriate weights
randomize: Boolean indicating whether to shuffle group labels - only set to TRUE when testing methods
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