Identify pairs of columns interacting with one another

Usage

asap_build_interaction_columns_mtx(
  mtx_file,
  row_file,
  col_file,
  idx_file,
  log_beta,
  beta_row_names,
  knn = 10L,
  mtx_file_rhs = NULL,
  row_file_rhs = NULL,
  col_file_rhs = NULL,
  idx_file_rhs = NULL,
  do_stdize_beta = TRUE,
  do_log1p = FALSE,
  verbose = TRUE,
  NUM_THREADS = 1L,
  CELL_NORM = 10000,
  BLOCK_SIZE = 1000L,
  MAX_ROW_WORD = 2L,
  ROW_WORD_SEP = "_",
  MAX_COL_WORD = 100L,
  COL_WORD_SEP = "@"
)

Arguments

mtx_file: matrix-market-formatted data file (D x N, bgzip)
row_file: row names file (D x 1)
col_file: column names file (N x 1)
idx_file: matrix-market colum index file
log_beta: D x K log dictionary/design matrix
beta_row_names: row names log_beta (D vector)
knn: How many nearest neighbours we want (default: 10)
mtx_file_rhs: right-hand-side matrix-market-formatted data file (bgzip)
row_file_rhs: right-hand-side row names (gene/feature names)
col_file_rhs: right-hand-side column names (cell/column names)
idx_file_rhs: right-hand-side matrix-market colum index file
do_stdize_beta: use standardized log_beta (Default: TRUE)
do_log1p: do log(1+y) transformation
verbose: verbosity
NUM_THREADS: number of threads in data reading
CELL_NORM: sample normalization constant (default: 1e4)
BLOCK_SIZE: disk I/O block size (number of columns)
MAX_ROW_WORD: maximum words per line in row_files[i]
ROW_WORD_SEP: word separation character to replace white space
MAX_COL_WORD: maximum words per line in col_files[i]
COL_WORD_SEP: word separation character to replace white space