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 1.2.0 Index]