pull_features: Generate simulated differential expression for two conditions

In kimberlyroche/codaDE: What the Package Does in One 'Title Case' Line

Generate simulated differential expression for two conditions

Description

Generate simulated differential expression for two conditions

Usage

pull_features(
  DE_methods = c("ALDEx2", "DESeq2", "scran"),
  use_baseline = "oracle",
  use_totals = FALSE,
  use_renorm_counts = FALSE,
  use_cpm = FALSE
)

Arguments

DE_methods	differential abundance calling methods to use
use_baseline	one of either "self" or "oracle"; baseline differential abundance calls against which we will score accuracy of calls made on observed (relative) abundance data
use_totals	pull fold change in total estimate from absolute counts
use_renorm_counts	pull features generated from method-renormalized data
use_cpm	use counts per million for relative abundances

Value

data.frame with predictive model training features

kimberlyroche/codaDE documentation built on May 11, 2022, 12:40 a.m.