Load well-level data written to binary format

This function loads well-level data written to binary files (.parquet and .rds) by the write_well_data_to_binary() function. The data contains sparse matrices (well x clone) of read counts for TCRalpha and TCRbeta along with metadata data frames for each clone.

Data loaded this way can be used as input to the plot_tshell() function.

Usage

load_well_counts_binary(folder, prefix, lazy = TRUE)

Arguments

folder

the directory with ".parquet" and ".rds" files written by write_well_data_to_binary()

prefix

a prefix with the sample name that will be prepended to the output file names

lazy

whether to "lazy load" the clone metadata files. This can speed up loading because these files are usually very large (default is TRUE).

Value

This function returns a list with the following elements:

• alpha - a sparse matrix ("dgCMatrix") of TCRalpha read counts in column-oriented format. See Matrix::`dgCMatrix-class`()

• beta - a sparse matrix ("dgCMatrix") of TCRbeta read counts in column-oriented format. See Matrix::`dgCMatrix-class`()

• alpha_meta - a data frame of clone metadata for TCRalpha clones. Row i relates to column i of alpha.

• beta_meta - a data frame of clone metadata for TCRbeta clones. Row i relates to column i of beta.

• col_meta - a data frame of well metadata (i.e. well names)

• alpha_meta_file - the file for the TCRalpha clone metadata

• beta_meta_file - the file for the TCRbeta clone metadata

See also

Other well: choose_pair_manual(), get_well_subset(), get_wells_from_edges(), plot_tshell(), write_well_data_to_binary()