ArchR2Signac: ArchR2Signac

In swaruplabUCI/ArchRtoSignac: What the Package Does (One Line, Title Case)

ArchR2Signac

Description

This function converts the ArchRProject to a SeuratObject by creating a list of Seurat objects for each sample with their corresponding peak matrix and then merging all of the objects in the list.

Usage

ArchR2Signac(
  ArchRProject,
  refversion,
  samples = NULL,
  fragments_dir = NULL,
  pm,
  fragments_fromcellranger = NULL,
  fragments_file_extension = NULL,
  annotation
)

Arguments

ArchRProject	An ArchRProject
refversion	The assembly release and versions of UCSC genome reference
samples	List of all the samples from the ArchRProject
fragments_dir	PATH to the cellranger-atac output–the folder that contains all samples folders, not the one with '/outs/fragments.tsv.gz'.
pm	Peak matrix (output) from the function getPeakMatrix
fragments_fromcellranger	This is an Yes or No selection ("NO" | "N" | "No" or "YES" | "Y" | "Yes")
fragments_file_extension	File_Extension for fragments files (typically they should be '.tsv.gz' or '.fragments.tsv.gz')
annotation	annotation from the function getAnnotation()

Examples

seurat_atac <- ArchR2Signac(ArchRProject = proj1, refversion = 'hg38', samples = samples, fragments_dir = fragments_dir, pm = pm, fragments_fromcellranger = "Yes", fragments_file_extension = NULL, annotation = annotations)

swaruplabUCI/ArchRtoSignac documentation built on Aug. 23, 2024, 2:03 p.m.