scCustomize (version 3.0.1)

Read_Metrics_10X: Read Overall Statistics from 10X Cell Ranger Count

Description

Get data.frame with all metrics from the Cell Ranger count analysis (present in web_summary.html)

Usage

Read_Metrics_10X(
  base_path,
  secondary_path = NULL,
  default_10X = TRUE,
  cellranger_multi = FALSE,
  lib_list = NULL,
  lib_names = NULL
)

Value

A data frame or list of data.frames with sample metrics from cell ranger.

Arguments

base_path

path to the parent directory which contains all of the subdirectories of interest or alternatively can provide single csv file to read and format identically to reading multiple files.

secondary_path

path from the parent directory to count "outs/" folder which contains the "metrics_summary.csv" file.

default_10X

logical (default TRUE) sets the secondary path variable to the default 10X directory structure.

cellranger_multi

logical, whether or not metrics come from Cell Ranger count or from Cell Ranger multi. Default is FALSE.

lib_list

a list of sample names (matching directory names) to import. If NULL will read in all samples in parent directory.

lib_names

a set of sample names to use for each sample. If NULL will set names to the directory name of each sample.

Examples

if (FALSE) {
metrics <- Read_Metrics_10X(base_path = "/path/to/directories", default_10X = TRUE)
}