bereFull: Bipartite Edge Reconstruction from Expression data (composite...

Description Usage Arguments Value Examples

Description

This function generates a complete bipartite network from gene expression data and sequence motif data

Usage

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bereFull(motifs, exprData, alpha = 0.5, penalized = TRUE, lambda = 10,
  score = "motifincluded")

Arguments

alpha

A weight parameter specifying proportion of weight to give to indirect compared to direct evidence. See documentation.

score

String to indicate whether motif information will be readded upon completion of the algorithm

motif

A motif dataset, a data.frame, matrix or exprSet containing 3 columns. Each row describes an motif associated with a transcription factor (column 1) a gene (column 2) and a score (column 3) for the motif.

expr

An expression dataset, as a genes (rows) by samples (columns) data.frame

verbose

logical to indicate printing of output for algorithm progress.

method

String to indicate algorithm method. Must be one of "cd","lda", or "wcd". Default is correlation difference "cd".

Value

TBD, An object of class "bere" (currently matrix or data.frame)

Examples

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dschlauch/MONSTER documentation built on May 15, 2019, 2:57 p.m.