Load CellBender h5 matrices (corrected) from multiple directories — Read_CellBender_h5_Multi

Extract sparse matrix with corrected counts from CellBender h5 output file across multiple sample subdirectories.

Read_CellBender_h5_Multi_Directory(
  base_path,
  secondary_path = NULL,
  filtered_h5 = TRUE,
  custom_name = NULL,
  sample_list = NULL,
  sample_names = NULL,
  h5_group_name = NULL,
  feature_slot_name = "features",
  replace_suffix = FALSE,
  new_suffix_list = NULL,
  parallel = FALSE,
  num_cores = NULL,
  merge = FALSE,
  ...
)

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 matrix files for each sample.
filtered_h5: logical (default TRUE). Will set the shared file name suffix custom_name is NULL.
custom_name: if file name was customized in CellBender then this parameter should contain the portion of file name that is shared across all samples. Must included the ".h5" extension as well.
sample_list: a vector of sample directory names if only specific samples are desired. If NULL will read in subdirectories in parent directory.
sample_names: a set of sample names to use for each sample entry in returned list. If NULL will set names to the subdirectory name of each sample.
h5_group_name: Name of the group within H5 file that contains count data. This is only required if H5 file contains multiple subgroups and non-default names. Default is NULL.
feature_slot_name: Name of the slot contain feature names/ids. Must be one of: "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".
replace_suffix: logical (default FALSE). Whether or not to replace the barcode suffixes of matrices using Replace_Suffix.
new_suffix_list: a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE. See Replace_Suffix for more information. To remove all suffixes set new_suffix_list = "".
parallel: logical (default FALSE) whether or not to use multi core processing to read in matrices.
num_cores: how many cores to use for parallel processing.
merge: logical (default FALSE) whether or not to merge samples into a single matrix or return list of matrices. If TRUE each sample entry in list will have cell barcode prefix added. The prefix will be taken from sample_names.
...: Extra parameters passed to Read_CellBender_h5_Mat.

Value

list of sparse matrices

Examples

if (FALSE) {
base_path <- 'path/to/data/directory'
mat_list <- Read_CellBender_h5_Multi_Directory(base_path = base_path)
}