compare_expression: Compare gene expression between two groups

In ChristophH/sctransform: Variance Stabilizing Transformations for Single Cell UMI Data

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
)

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

Value

Data frame of results

ChristophH/sctransform documentation built on Oct. 22, 2023, 3:28 p.m.