Read_Metrics_10X {scCustomize} | R Documentation |
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
)
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 |
lib_list |
a list of sample names (matching directory names) to import. If |
lib_names |
a set of sample names to use for each sample. If |
Value
A data frame with sample metrics from cell ranger.
Examples
## Not run:
metrics <- Read_Metrics_10X(base_path = "/path/to/directories", default_10X = TRUE)
## End(Not run)