Convert10Xfolders.old: Convert10Xfolders.old

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

Convert10Xfolders.old

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.old(
  InputDir,
  folderPattern = c("filtered", "SoupX_decont")[1],
  min.cells = 10,
  min.features = 200,
  updateHGNC = TRUE,
  ShowStats = TRUE
)

Arguments

InputDir	A character string specifying the input directory.
folderPattern	A character vector specifying the pattern of folder names to be searched. Default: 'filtered'.
min.cells	An integer value specifying the minimum number of cells. Default: 10.
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.

Examples

## Not run: 
if (interactive()) {
  Convert10Xfolders.old(InputDir = InputDir)
}

## End(Not run)

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