coAccess: coAccess

In plantformatics/Socrates: Analysis of scATAC-seq data

coAccess

Description

This function identifies co-accessible ACRs within clusters or across the entire data set

Usage

coAccess(
  obj,
  genome = NULL,
  byGroup = FALSE,
  groupID = "LouvainClusters",
  eFDR = FALSE,
  fdr_thresh = 0.05,
  win_size = 5e+05,
  sample_num = 100,
  k = 30,
  conn_slotName = "coACRs",
  nthreads = 1,
  verbose = FALSE
)

Arguments

obj	Socrates object. Required.
genome	path to genome file. See 'inst/extdata/genome' for an example. Required.
byGroup	logical. Whether to run co-accessibility tests for each factor in 'groupID'. Defaults to False.
groupID	character. Column name in obj$meta for partitioning during co-accessibility analysis. Defaults to "LouvainClusters".
eFDR	logical. Whether or not to use empirical FDR to filter co-accessible ACRs. Defaults to FALSE. Setting eFDR to 'TRUE' doubles memory usage.
fdr_thresh	float. fdr threshold when using empirical FDR. Defaults to 0.05.
win_size	numeric. Genomic distance to constrain co-accessible ACRs. Defaults to 500000.
sample_num	numeric. Number of random windows to sample for determining distance_parameter during 'run_cicero'. See cicero for more details.
k	numeric. Number of nearest neighbors for aggregating cells. Defaults to 30.
conn_slotName	character. Slot name for depositing co-accessible ACRs. Defaults to coACRs.
nthreads	numeric. Number of threads to use for estimating co-ACRs for each cluster or celltype. Defaults to 1.
verbose	logical. Defaults to FALSE.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.