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PMF regression

asap_pmf_regression_mtx.Rd

PMF regression

Usage

asap_pmf_regression_mtx(
  mtx_file,
  row_file,
  col_file,
  idx_file,
  log_beta,
  beta_row_names,
  r_log_delta = NULL,
  do_stdize_beta = TRUE,
  do_stdize_r = TRUE,
  do_log1p = FALSE,
  a0 = 1,
  b0 = 1,
  max_iter = 10L,
  verbose = FALSE,
  NUM_THREADS = 0L,
  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 (default: TRUE)

beta_row_names

row names log_beta (D vector)

r_log_delta

D x B log batch effect matrix

do_stdize_beta

use standardized log_beta (Default: FALSE)

do_stdize_r

standardize correlation matrix R (default: TRUE)

do_log1p

do log(1+y) transformation

a0

gamma(a0, b0) (default: 1)

b0

gamma(a0, b0) (default: 1)

max_iter

maximum iterations (default: 10)

verbose

verbosity

NUM_THREADS

number of threads in data reading

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

Value

a list that contains:

  • beta dictionary matrix (row x factor)

  • delta the dictionary matrix of batch effects (row x batch)

  • corr empirical correlation (column x factor)

  • theta factor loading (column x factor)

  • log.theta log-scaled factor loading (column x factor)

  • colsum the sum of each column (column x 1)

  • rownames row/feature names

  • colnames column/sample names