attractorScanning: Find all attractors in the dataset
In weiyi-bitw/cafr: Attractor Metagenes Finding Algorithm

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Exhaustively search for all attractors in the dataset.

1	attractorScanning(data, a=5, maxIter=100, epsilon=1E-14, bin=6, so=3, rankBased=FALSE, negateMI=TRUE)

`data`	An expression matrix with genes in the rows, samples in the columns.
`a`	Exponent of the mutual information, used to create weight vector for metagenes.
`maxIter`	Max number of iterations.
`epsilon`	Threshold of convergence.
`bin`	Number of bins used when estimate mutual information (default=6).
`so`	Spline order used when estimate mutual information (default=3).
`rankBased`	When `TRUE`, convert the expression values into ranks.
`negateMI`	When `TRUE`, negate the mutual information if the two vectors have negative momentum.

attractorScanning searches for all the attractors in the dataset by applying CAFrun using every gene as a seed in the dataset. It will ignore the attractors which were dominated by the seed gene. As the function finds a new attractor, it removes the genes from the search list that are more significant (with higher MI) than the seed, due to that they will lead to the same attractor. Therefore the size of the search list decreases exponentially during the process.

During the search process, the program shows its progress by the lines:

CENPA ( 10 / 300 ) ...

which shows the current seed (CENPA), the number of attractor it tries to finds (10th), the number of seeds left to be searched (300).

Returns a matrix of size k by m, where m is the number of genes (rows) in the dataset, and k the number of converged attractors. Each row of the matrix is the MI of all the genes with the converged attractor.

Missing values are not allowed as the input to the function in the current version.

Wei-Yi Cheng

Wei-Yi Cheng, Tai-Hsien Ou Yang and Dimitris Anastassiou, Biomolecular events in cancer revealed by attractor metagenes, PLoS Computational Biology, Vol. 9, Issue 2, February 2013.

parAttractorScanning for excuting attractorScanning on SGE framework. findAttractor, attractorScanningGL

## Not run: 
# Load the toy dataset extracted from TCGA OV data
data(ov)

# find attractor using CENPA as a seed
as <- attractorScanning(ov)

# display the top 20 genes in first attractor
sort(as[1,], decreasing=TRUE)[1:20]

## End(Not run)