compareGenes: Union and intersection of contributing genes

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

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 typeGenes_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)

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.