RunBicluster: RunBicluster

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Description

This function will identify the Biclusters based on LTMG or Quantile normalization

Usage

RunBicluster(object, ...)

.runBicluster(
  object = NULL,
  DiscretizationModel = "Quantile",
  OpenDual = FALSE,
  Extension = 1,
  NumBlockOutput = 100,
  BlockOverlap = 0.7,
  BlockCellMin = 15
)

## S4 method for signature 'IRISFGM'
RunBicluster(
  object = NULL,
  DiscretizationModel = "Quantile",
  OpenDual = FALSE,
  Extension = 1,
  NumBlockOutput = 100,
  BlockOverlap = 0.7,
  BlockCellMin = 15
)

Arguments

object	input IRIS-FGM object
...	other arguments passed to methods
DiscretizationModel	use different discretization method, including 'Quantile' and 'LTMG.'
OpenDual	the flag using the lower bound of condition number. Default: 5 percent of the gene number in current bicluster.
Extension	consistency level of the block (0.5-1.0], the minimum ratio between the number of identical valid symbols in a column and the total number of rows in the output. Default: 1.0.
NumBlockOutput	number of blocks to report. Default: 100.
BlockOverlap	filtering overlapping blocks. Default: 0.7.
BlockCellMin	minimum column width of the block. Default: 15 columns.

Value

It will generate a temporal file on local directory for processed data named 'tmp_expression.txt', discretized file named 'tmp_expression.txt.chars', and biclsuter block named 'tmp_expression.txt.chars.block'.

Examples

# based on LTMG discretization
## Not run: 
object <- RunBicluster(object, 
DiscretizationModel = 'LTMG',
OpenDual = F,
NumBlockOutput = 1000, 
BlockOverlap = 0.7, 
BlockCellMin = 15)

## End(Not run)
# based on quantile discretization
## Not run: 
object <- RunBicluster(object, 
DiscretizationModel = 'Quantile',
OpenDual = F, 
NumBlockOutput = 1000, 
BlockOverlap = 0.7, 
BlockCellMin = 15)

## End(Not run)

carter-allen/IRISFGM documentation built on Dec. 31, 2020, 9:54 p.m.