matchGeneSets {GRridge} | R Documentation

## Creates a grouping of variables (genes) from gene sets

### Description

Creates a grouping of variables (genes) from gene sets by matching the IDs of the genes with the IDs of the members of the gene sets

### Usage

    matchGeneSets(GeneIds, GeneSets, minlen = 25, remain = TRUE)

### Arguments

`GeneIds` | Character vector. Vector of gene IDs. Can be any ID (gene symbol, entrezID, etc) as long as it matches with IDs used in `GeneSets`.
`GeneSets` | Named list of character vectors. Each component of the list represents a named gene set. Each vector a list of member genes.
`minlen` | Integer. Minimum number of members of a gene set.
`remain` | Boolean. If `remain=TRUE`, all genes that are not in any list will be grouped in one remainder group.

### Details

About `minlen`: to avoid overfitting in the `grridge` function, we recommend to not use groups with less than 25 members, unless `monotone=TRUE` is used in the `grridge` function, in which case 10 members may suffice as a lower bound. About `remain`: it is often beneficial to down-weight genes that are not part of any gene set, so we recommend to use `remain=TRUE`

### Value

A list the components of which contain the indices of the variables belonging to each of the groups.

### Author(s)

Mark A. van de Wiel

### See Also

`grridge`, `CreatePartition`

### Examples

    # Load data objects
    data(dataWurdinger)

    # Transform the data set to the square root scale
    dataSqrtWurdinger <- sqrt(datWurdinger_BC)

    #Standardize the transformed data
    datStdWurdinger <- t(apply(dataSqrtWurdinger,1,function(x){(x-mean(x))/sd(x)}))

    # A list of gene names in the primary RNAseq data
    genesWurdinger <- as.character(annotationWurdinger$geneSymbol)

    # We  show an example of GRridge classification model by using overlapping groups,
    # i.e. pathway-based grouping. Transcription factor based pathway was extracted from
    # the MSigDB (Section C3: motif gene sets; subsection: transcription factor targets;
    # file's name: "c3.tft.v5.0.symbols.gmt"). The gene sets are based on
    # TRANSFAC version 7.5 database (http://www.gene-regulation.com/).

    # Some features may belong to more than one group. The argument minlen=25 implies
    # the minimum number of features in a gene set. If remain=TRUE, gene sets with less
    # than 25 members are grouped to the "remainder" group. "genesWurdinger" is an object
    # containing gene names from the mRNA sequencing data set.
    # See help(matchGeneSets) for more detail information.
    # Also see Vignette for more detail examples

    ## The "TFsym" is available on https://github.com/markvdwiel/GRridgeCodata
    # gseTF <- matchGeneSets(genesWurdinger,TFsym,minlen=25,remain=TRUE)

[Package GRridge version 1.4.0 Index]