Convert10Xfolders_v1: Convert10Xfolders - legacy version

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Convert10Xfolders - legacy version

Description

This function takes a parent directory with a number of subfolders, each containing the standard output of 10X Cell Ranger. It (1) loads the filtered data matrices, (2) converts them to Seurat objects, and (3) saves them as .RDS files.

Usage

Convert10Xfolders_v1(
  InputDir,
  regex = FALSE,
  folderPattern = c("filtered_feature", "raw_feature", "SoupX_decont")[1],
  depth = 4,
  min.cells = 5,
  min.features = 200,
  updateHGNC = TRUE,
  ShowStats = TRUE,
  writeCBCtable = TRUE,
  sample.barcoding = FALSE,
  nthreads = .getNrCores(),
  preset = "high",
  ext = "qs",
  sort_alphanumeric = TRUE,
  ...
)

Arguments

InputDir	A character string specifying the input directory.
regex	A logical value. If TRUE, the folderPattern is treated as a regular expression. Default: FALSE.
folderPattern	A character vector specifying the pattern of folder names to be searched. Default: 'filtered_feature'.
depth	An integer value specifying the depth of scan (i.e., how many levels below the InputDir). Default: 2.
min.cells	An integer value specifying the minimum number of cells. Default: 5.
min.features	An integer value specifying the minimum number of features. Default: 200.
updateHGNC	A logical value indicating whether to update the HGNC. Default: TRUE.
ShowStats	A logical value indicating whether to show statistics. Default: TRUE.
writeCBCtable	A logical value indicating whether to write out a list of cell barcodes (CBC) as a tsv file. Default: TRUE.
sample.barcoding	A logical value indicating whether Cell Ranger was run with sample barcoding. Default: FALSE.
sort_alphanumeric	sort files alphanumeric? Default: TRUE.

Examples

## Not run: 
if (interactive()) Convert10Xfolders(InputDir)

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.