PBE_MERGE: Progressive extension and merging of biclusters

In unistbig/bimir: Condition-Specific microRNA Target Prediction by Biclustering of Large Transcriptome Data

Description

Progressive extension and merging of biclusters

Usage

PBE_MERGE(MIR_profile, mir, biclust.path = "./", FCcutoff = log2(1.3),
  REPETITION = 10, STEP_NUMBER = 10, ZERORATE = 0.1, tree_cutoff = 0.5)

Arguments

MIR_profile	A matrix of microRNA profile where rows are cell conditions and columns are sequence-based miRNA targets.
mir	Name of microRNA
biclust.path	Directory where biclusts will be saved
FCcutoff	Log2-fold change binarization cutoff for seed. Default = log2(1.3)
REPETITION	The number of repetition that the ensemble function runs to extract seed biclusters. Default = 10
STEP_NUMBER	The number of extension process. Default = 10
ZERORATE	Final zero rate allowed. Default = 0.1
tree_cutoff	Similarity cutoff. Default = 0.5

Value

Extended and merged biclusters in the directory assigned to ‘biclust.path’.

unistbig/bimir documentation built on May 29, 2019, 8:03 a.m.