correlateTrajectories: Correlate Trajectories
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

correlateTrajectories

R Documentation

Correlate Trajectories

Description

This function will correlate 2 trajectory matrices from getTrajectory.

Usage

correlateTrajectories(
  seTrajectory1 = NULL,
  seTrajectory2 = NULL,
  corCutOff = 0.5,
  varCutOff1 = 0.8,
  varCutOff2 = 0.8,
  removeFromName1 = c("underscore", "dash"),
  removeFromName2 = c("underscore", "dash"),
  useRanges = FALSE,
  fix1 = "center",
  fix2 = "start",
  maxDist = 250000,
  log2Norm1 = TRUE,
  log2Norm2 = TRUE,
  force = FALSE,
  logFile = createLogFile("correlateTrajectories")
)

Arguments

`seTrajectory1`	A `SummarizedExperiment` object that results from calling `getTrajectory()`.
`seTrajectory2`	A `SummarizedExperiment` object that results from calling `getTrajectory()`.
`corCutOff`	A numeric describing the cutoff for determining correlated features.
`varCutOff1`	The "Variance Quantile Cutoff" to be used for identifying the top variable features across `seTrajectory1`. Only features with a variance above the provided quantile will be retained.
`varCutOff2`	The "Variance Quantile Cutoff" to be used for identifying the top variable features across `seTrajectory2`. Only features with a variance above the provided quantile will be retained.
`removeFromName1`	A character vector describing how to filter names in matrix 1. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept.
`removeFromName2`	A character vector describing how to filter names in matrix 2. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept.
`useRanges`	A boolean describing whether to use range overlap matching for correlation analysis.
`fix1`	A character describing where to resize the coordinates of `seTrajectory1`. Options include "start", "center", "end".
`fix2`	A character describing where to resize the coordinates of `seTrajectory2`. Options include "start", "center", "end".
`maxDist`	A integer specifying the maximum distance between the coordinates of `seTrajectory1` and `seTrajectory2` for computing correlations.
`log2Norm1`	A boolean describing whether to log2 normalize `seTrajectory1`.
`log2Norm2`	A boolean describing whether to log2 normalize `seTrajectory2`.
`force`	A boolean value that determines whether analysis should continue if resizing coordinates in `seTrajectory1` or `seTrajectory2` does not align with the strandedness. Only when `useRanges = TRUE`.
`logFile`	The path to a file to be used for logging ArchR output.

Examples


# Get Test ArchR Project
proj <- getTestProject()

#Add Trajectory
proj <- addTrajectory(proj, trajectory = c("C1", "C2", "C3"), embedding = "UMAP", force = TRUE)

#Get Trajectories
seTraj1 <- getTrajectory(proj, useMatrix = "GeneScoreMatrix")
seTraj2 <- getTrajectory(proj, useMatrix = "GeneIntegrationMatrix")

#Correlate
corTraj <- correlateTrajectories(seTraj1, seTraj2, corCutOff = 0.35, varCutOff1 = 0.6, varCutOff2 = 0.6)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.