RunBicluster {IRISFGM}R Documentation

RunBicluster

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
data("example_object")
example_object<- RunLTMG(example_object,Gene_use = "200")
example_object <- CalBinaryMultiSignal(example_object)
# Due to generate intermedie files, please make sure to set working directory

example_object <- RunBicluster(example_object, 
                              DiscretizationModel = 'LTMG',
                              OpenDual = FALSE,
                              NumBlockOutput = 1000, 
                              BlockOverlap = 0.7, 
                              BlockCellMin = 15)
                              



[Package IRISFGM version 1.1.1 Index]