Skip to contents

Generate approximate pseudo-bulk data by random projections while sharing columns/cells across multiple data sets. Vertical concatenation.

Usage

asap_random_bulk_rbind_mtx(
  mtx_files,
  row_files,
  col_files,
  idx_files,
  num_factors,
  rseed = 42L,
  verbose = TRUE,
  NUM_THREADS = 1L,
  CELL_NORM = 10000,
  BLOCK_SIZE = 1000L,
  do_log1p = FALSE,
  do_down_sample = FALSE,
  save_rand_proj = FALSE,
  weighted_rand_proj = FALSE,
  CELL_PER_SAMPLE = 100L,
  a0 = 1e-08,
  b0 = 1,
  MAX_ROW_WORD = 2L,
  ROW_WORD_SEP = "_",
  MAX_COL_WORD = 100L,
  COL_WORD_SEP = "@"
)

Arguments

mtx_files

matrix-market-formatted data files (bgzip)

row_files

row names (gene/feature names)

col_files

column names (cell/column names)

idx_files

matrix-market colum index files

num_factors

a desired number of random factors per data set

rseed

random seed

verbose

verbosity

NUM_THREADS

number of threads in data reading

CELL_NORM

normalization constant per each data point

BLOCK_SIZE

disk I/O block size (number of columns)

do_log1p

log(x + 1) transformation (default: FALSE)

do_down_sample

down-sampling (default: FALSE)

save_rand_proj

save random projection (default: FALSE)

weighted_rand_proj

save random projection (default: FALSE)

CELL_PER_SAMPLE

down-sampling cell per sample (default: 100)

a0

gamma(a0, b0) (default: 1e-8)

b0

gamma(a0, b0) (default: 1)

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

Value

a list

  • PB.list pseudobulk (average) data (feature x sample) for each type

  • sum.list pseudobulk (sum) data (feature x sample) for each type

  • size.list size per sample (sample x 1) for each type

  • rownames.list feature (gene) names for each type

  • colnames column (cell) names across data types

  • positions pseudobulk sample positions (cell x 1)

  • rand.proj random projection results (sample x proj factor)

  • colnames column (cell) names