gibbsSampler {CDSeq}R Documentation

This is the Gibbs sampler for CDSeq. GibbsSampler returns estimated GEPs and cell type proportions.

Description

This is the Gibbs sampler for CDSeq. GibbsSampler returns estimated GEPs and cell type proportions.

Usage

gibbsSampler(
  ALPHA,
  BETA,
  mixtureSamples,
  T,
  NN,
  OUTPUT,
  processID,
  data_block_idx,
  CDSeq_tmp_log,
  write_2_file,
  verbose
)

Arguments

ALPHA

hyperparameter for cell type proportion.

BETA

hyperparameter for cell-type-specific GEPs.

mixtureSamples

bulk RNA-seq data in form of read counts.

T

number of cell types.

NN

number of MCMC iteration.

OUTPUT

MCMC progress output control.

processID

worker process ID when using parallel computing.

data_block_idx

index for data blocks from bulk RNA-seq input.

CDSeq_tmp_log

temporary log file recording the workers' jobs.

write_2_file

print to progress msg to CDSeq_tmp_log if it is 1, not printing otherwise.

verbose

if greater than or euqal to 1, then print working progress in console, otherwise do not print in console.

Value

random integers uniformly distributed in 0..(2^32 - 1).


[Package CDSeq version 1.0.8 Index]