compareGenes: Union and intersection of contributing genes
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Value Author(s) See Also Examples

Compute and annotate the intersection or union between contributiong genes of components originating from different IcaSet objects.

  compareGenes(keepCompByIcaSet, icaSets, lab, cutoff = 0,
    type = c("union", "intersection"), annotate = TRUE,
    file,
    mart = useMart("ensembl", "hsapiens_gene_ensembl"))

`icaSets`	List of `IcaSet` objects, the `geneNames` of the `IcaSet` objects must be from the same type (e.g, gene Symbols).
`keepCompByIcaSet`	Indices of the components to be considered in each `IcaSet`.
`lab`	The names of the icaSets (e.g the names of the datasets they originate from).
`cutoff`	The cutoff (on the absolute centered and scaled projections) above which the genes have to be considered.
`type`	`"intersection"` to restrict the list of genes to the ones that are common between all datasets, or `"union"` to consider all the union of genes available across the datasets.
`annotate`	If TRUE (default) the genes are annotated using function `writeGenes`.
`file`	The HTML file name where the genes and their annotations are written, default is `type`Genes_lab1-i_lab2-j_... where i and j are the component indices contained in `keepCompByIcaSet`.
`mart`	The mart object (database and dataset) used for annotation, see function `useMart` of package `biomaRt`.

A data.frame containing

typeID(icaSets[[1]])['geneID_biomart']:: the gene IDs,
median_rank: the median of the ranks of each gene across the IcaSet objects,
analyses: the labels of the IcaSet objects in which each gene is above the given cutoff
min_rank: the minimum of the ranks of each gene across the IcaSet objects,
ranks: the ranks of each gene in each IcaSet where it is available,
scaled_proj: the centered and reduced projection of each gene in each IcaSet where it is available.

Anne Biton

writeGenes

## Not run: 
data(icaSetCarbayo)
mart <- useMart("ensembl", "hsapiens_gene_ensembl")

## comparison of two components
## here the components come from the same IcaSet for convenience
## but they must come from different IcaSet in practice.
compareGenes(keepCompByIcaSet = c(9,4), icaSets = list(icaSetCarbayo, icaSetCarbayo),
             lab=c("Carbayo", "Carbayo2"), cutoff=3, type="union",  mart=mart)


## End(Not run)