stat_test_expression: Perform statistical test on median expression values across...

In kordastilab/ImmunoCluster: Fast and accesible Immune profiling CyTOF data

Description

Perform statistical test on median expression values across clusters and conditions. Generates p adjusted values with "BH" p.adjust method.

Usage

stat_test_expression(
  indata,
  assay = "scaled",
  grouping = "group",
  feature = "condition",
  clusterAssign = "cell_annotation",
  test = "wilcox",
  var_equal = TRUE
)

Arguments

indata	a SingleCellExperiment.
assay	the assay to select from the sce.
grouping	the sample_ids to generate the median expression from.
feature	the feature to test the median expression data between.
clusterAssign	the clustering to generate the median expression from.
test	either 'wilcox' calls pairwise.wilcox.test or 't_test' calls pairwise.t.test.
var_equal	sets the pool.sd parameter to apply welch's correction as a parameter of pairwise.t.test

Value

a dataframe containing the median marker expression per cluster-marker and sample along with pval and BH adjusted pvalue.

kordastilab/ImmunoCluster documentation built on May 10, 2021, 7:41 a.m.