compareGenes {MineICA} | R Documentation

## Union and intersection of contributing genes

### Description

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

### Usage

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

### Arguments

`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`.

### Value

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.

### Author(s)

Anne Biton

### See Also

`writeGenes`

### Examples

    ## 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)

[Package MineICA version 1.32.0 Index]