add_tde_overall: Add information on overall differentially expressed features

In dynwrap: Representing and Inferring Single-Cell Trajectories

Add information on overall differentially expressed features

Description

To calculate differential expression within trajectories, check out the dynfeature package.

Usage

add_tde_overall(trajectory, tde_overall)

Arguments

trajectory	The trajectory as created by infer_trajectory() or add_trajectory()
tde_overall	A dataframe containing the feature_id, and some other columns including whether it is differentially expressed (differentially_expressed), the rank of differential expression among all other features (rank), the p-value (pval) or corrected value (qval), and the log-fold change (lfc).

Value

A trajectory containing tde_overall, a dataframe containing the feature_id, and some other columns including whether it is differentially expressed (differentially_expressed), the rank of differential expression among all other features (rank), the p-value (pval) or corrected value (qval), and the log-fold change (lfc).

Examples

trajectory <- example_trajectory
tde_overall <- tibble::tibble(
  feature_id = trajectory$feature_info$feature_id,
  differentially_expressed = sample(c(TRUE, FALSE), length(feature_id), replace = TRUE)
)
trajectory <- add_tde_overall(trajectory, tde_overall)
trajectory$tde_overall

dynwrap documentation built on July 26, 2023, 5:15 p.m.