Read Overall Statistics from 10X Cell Ranger Count

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

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

Arguments

base_path

path to the parent directory which contains all of the subdirectories of interest.

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.

Value

A data frame with sample metrics from cell ranger.

Examples

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