grnscores-methods: Compute and plot GRN scores for transcriptional regulators.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Compute and plot GRN scores for transcriptional regulators.

Description

Compute and plot the GRN scores of most representative genes in trajectories and save to file. Integrate gene regulatory networks with gene expression dynamics along the trajectories to calculate a GRN score and identify putative regulators of these cell-fate transitions.

Usage

grnscores(
  object,
  ggrn,
  tfs,
  transitions,
  direction = c("up", "down", "both"),
  dir.targets = c("up", "down"),
  q.up = 0.95,
  q.down = 0.05,
  flip
)

## S4 method for signature 'CellRouter'
grnscores(
  object,
  ggrn,
  tfs,
  transitions,
  direction = c("up", "down", "both"),
  dir.targets = c("up", "down"),
  q.up = 0.95,
  q.down = 0.05,
  flip
)

Arguments

object	CellRouter object.
ggrn	igraph; the gene regulatory network.
tfs	character vector; gene names of transcriptional regulators.
transitions	character vector; selected transitions of interest.
direction	character; plot genes up-regulated, down-regulated or both along trajectories.
dir.targets	character; whether the predicted targets are up or down-regulated.
q.up	numeric; cutoff to select top q.up transcriptional regulators.
q.down	numeric; cutoff to select top q.down transcriptional regulators.
flip	boolean; apply coordinate flip (horizontal and vertical) to the plot.

Value

list; all scores list with scores and targets, and plots.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.