sctransform (version 0.4.3)

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
)

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 method = '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 the verbosity level: 0 (silent, no messages), 1 (show messages only), or 2 (show messages and progress bars); default is 2