ComputeClustersByTrt: Given a Seurat object and treatment variable, compare...

In daskelly/signac: Extensions to Seurat

Given a Seurat object and treatment variable, compare clusters between levels of the treatment

Description

Given a Seurat object and treatment variable, compare clusters between levels of the treatment

Usage

ComputeClustersByTrt(
  obj,
  trt_var,
  rep_var,
  group_by = NULL,
  ci = TRUE,
  ci_alpha = 0.05
)

Arguments

obj	Seurat object
trt_var	Treatment variable
rep_var	Replicate/Individual ID variable
group_by	Name of grouping variable (default is Idents)
ci	Whether to plot binomial confidence intervals (Jeffreys)

Examples

pbmc_small$trt <- sample(c('drug', 'control'), ncol(pbmc_small), replace=TRUE)
pbmc_small$genotype <- sample(c('1', '2', '3'), ncol(pbmc_small), replace=TRUE)
head(ComputeClustersByTrt(pbmc_small, trt, genotype))

daskelly/signac documentation built on Feb. 12, 2023, 11:36 p.m.