Generate a list of GRaNIE objects from a root directory that has been originally generated with prepareSeuratData_GRaNIE and for which subsequently GRaNIE has been run for.

Either this or generateGRNList_custom can be used to automatically populate a list with GRaNIE objects for further analysis using the functions from this package that have the GRN.list argument.

generateGRNList_Seurat(
  rootDir,
  prefix = "output_pseudobulk_clusterRes",
  resolutions = NULL,
  suffix = "_RNA_limma_quantile_ATAC_DESeq2_sizeFactors",
  compression = c("qs", "rds"),
  slotsToDelete = c("annotation", "visualization", "graph", "stats", "data")
)

Arguments

rootDir

Character string specifying the root directory in which the GRaNIE objects are located

prefix

Character string specifying the prefix of the file names to look for. Default is `"output_pseudobulk_clusterRes"`.

resolutions

Numeric vector specifying the resolutions to consider. Default is `NULL`, which means all resolutions will be considered.

suffix

Character string specifying the suffix of the file names to look for. Default is `"_RNA_limma_quantile_ATAC_DESeq2_sizeFactors"`.

compression

Character vector specifying the file compression formats to look for. Options are `"qs"` and `"rds"`. Default is both.

slotsToDelete

Character vector specifying the slots to delete from the Seurat objects to save memory. Default includes `"annotation"`, `"visualization"`, `"graph"`, `"stats"`, and `"data"`.

Value

A list of GRN objects generated from the GRaNIE objects found in the specified directory.