FindMarkersFlex: Test for markers flexibly from a Seurat object.

In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data

Description

Calls FindMarkers with extra features.

Usage

FindMarkersFlex(object, ident.use, ident.1, ident.2 = object %>%
  FetchData(ident.use) %>% extract2(1) %>% unique %>% setdiff(ident.1),
  order_by_var = "avg_diff", thresh.use = 0.25,
  test.use = "binomial_batch", genes.use = object@data %>% rownames,
  min.pct = 0.1, ...)

Arguments

ident.use	Fetched via FetchData to define the groups being tested. Should obey
test.use	Passed into FindMarkers unless it is "binomial_batch", in which case it uses approximate p-values based on a binomial glmm with a random effect for batch (1|orig.ident). All other parameters are passed into FindMarkers unless test.use=="binomial_batch", in which case I attempt to match the behavior of FindMarkers. Output contains an extra column for q-values from p.adjust(..., method="fdr").

maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.