relNetworkB {maigesPack} | R Documentation

## Relevance Network analysis

### Description

Function to construct Relevance Networks for one biological type (Butte's Relevance Network).

### Usage

    relNetworkB(data=NULL, gLabelID="GeneName", sLabelID="Classification",
                geneGrp=NULL, path=NULL, samples=NULL,
                type="Rpearson", bRep=1000, ...)

### Arguments

`data` | object of class `maiges`.
`gLabelID` | character string giving the identification of gene label ID.
`sLabelID` | character string giving the identification of sample label ID.
`geneGrp` | character string (or numeric index) specifying the gene group to calculate the correlation values between them. If NULL (together with path) all genes are used.
`path` | character string (or numeric index) specifying the gene network to calculate the correlation values between them. If NULL (together with geneGrp) all genes are used.
`samples` | a character vector specifying the group to be compared.
`type` | type of correlation to be calculated. May be 'Rpearson' (default), 'pearson', 'kendall', 'spearman' or 'MI'.
`bRep` | integer specifying the number of bootstrap permutation to calculate the significance of correlation values.
`...` | additional parameters for functions `robustCorr` or `cor`.

### Details

This method uses the function `cor` to calculate the usual correlation values, `robustCorr` to calculate a robust correlation using an idea similar to the leave-one-out or `MI` to calculate mutual information values.

### Value

The result of this function is an object of class `maigesRelNetB`.

### Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

### References

Butte, A.J. and Kohane, I.S. Unsupervised Knowledge discovery in medical databases using relevance networks. In Proc. AMIA Symp., 711-715, 1999 (http://www.amia.org/pubs/symposia/D005550.HTM)

Butte, A.J.; Tamayo, P.; Slonim, D.; Golub, T.R. and Kohane, I.S. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks, PNAS, 97, 12182-12186, 2000 (http://www.pnas.org/cgi/content/full/97/22/12182)

Butte, A.J. and Kohane, I.S. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. In Pacific Symposium on Biocomputing, 5, 415-426, 2000 (http://psb.stanford.edu/psb-online/proceedings/psb00/)

### See Also

`cor`, `robustCorr`, `MI` `maigesRelNetB`, `plot.maigesRelNetB`, `image.maigesRelNetB`.

### Examples

    ## Loading the dataset
    data(gastro)

    ## Constructing the relevance network (Butte's method) for sample
    ## 'Tissue' equal to 'Neso' for the 1st gene group
    gastro.net = relNetworkB(gastro.summ, sLabelID="Tissue",
      samples="Neso", geneGrp=1, type="Rpearson")

    ## Constructing the relevance network (Butte's method) for sample
    ## 'Type' equal to 'Col' for the 1st gene group using the conventional
    ## pearson correlation
    gastro.net = relNetworkB(gastro.summ, sLabelID="Type",
      samples="Col", geneGrp=1, type="pearson")

[Package maigesPack version 1.4.0 Index]