CreatePartition {GRridge} | R Documentation

## Creates a partition (groups) of variables

### Description

Creates a partition (groups) of variables from nominal (factor) or numeric input

### Usage

    CreatePartition(vec,varnamesdata=NULL,subset=NULL,grsize=NULL,
                    decreasing=TRUE,uniform=FALSE,ngroup=10,mingr=25)

### Arguments

`vec` | Factor, numeric vector or character vector.
`subset` | Character vector. Names of variables (features) that correspond to the values in `vec`. Allows to make a partition on a subset of all variables. Requires `varnamesdata`.
`varnamesdata` | Character vector. Names of the variables (features). Only relevant when `vec` is a character vector OR when `subset` is specified.
`grsize` | Numeric. Size of the groups. Only relevant when `vec` is a numeric vector and `uniform=TRUE`.
`decreasing` | Boolean. If `TRUE` then `vec` is sorted in decreasing order.
`uniform` | Boolean. If `TRUE` the group sizes are as equal as possible.
`ngroup` | Numeric. Number of the groups to create. Only relevant when `vec` is a numeric vector and `grsize` is NOT specified.
`mingr` | Numeric. Minimum group size. Only relevant when `vec` is a numeric vector and `uniform=FALSE`.

### Details

A convenience function to create partitions of variables from external information that is stored in `vec`. If `vec` is a factor then the levels of the factor define the groups. If `vec` is a character vector, then `varnamesdata` need to be specified (`vec` is supposed to be a subset of `varnamesdata`, e.g. a published gene list). In this case a partition of two groups is created: one with those variables of `varnamesdata` that also appear in `vec` and one which do not appear in `vec`. If `vec` is a numeric vector, then groups contain the variables corresponding to `grsize` consecutive values of the values in `vec`. Alternatively, the group size is determined automatically from `ngroup`. If `uniform=FALSE`, a group with rank $r$ is of approximate size `mingr*(r^f)`, where `f>1` is determined such that the total number of groups equals `ngroup`. Such unequal group sizes enable the use of fewer groups (and hence faster computations) while still maintaining a good ‘resolution’ for the extreme values in `vec`. About `decreasing`: if smaller values of components of `vec` mean ‘less relevant’ (e.g. test statistics, absolute regression coefficients) use `decreasing=TRUE`, else use `decreasing=FALSE`, e.g. for p-values. If `subset` is defined, then `varnamesdata` should be specified as well. The parition will then only be applied to variables in `subset` and in `varnamesdata`.

### 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

For gene sets (overlapping groups): `matchGeneSets`. Further example in real life dataset: `grridge`.

### Examples

    #SOME EXAMPLES ON SMALL NR OF VARIABLES

    #EXAMPLE 1: partition based on known gene signature
    genset <- sapply(1:100,function(x) paste("Gene",x))
    signature <- sapply(seq(1,100,by=2),function(x) paste("Gene",x))
    SignaturePartition <- CreatePartition(signature,varnamesdata=genset)

    #EXAMPLE 2: partition based on factor variable
    Genetype <- factor(sapply(rep(1:4,25),function(x) paste("Type",x)))
    TypePartition <- CreatePartition(Genetype)

    #EXAMPLE 3: partition based on continuous variable, e.g. p-value
    pvals <- rbeta(100,1,4)

    #Creating a partition of 10 equally-sized groups, corresponding to increasing p-values.
    PvPartition <- CreatePartition(pvals, decreasing=FALSE,uniform=TRUE,ngroup=10)

    #Alternatively, create a partition of 5 unequally-sized groups,
    #with minimal size at least 10. Group size
    #increases with less relevant p-values.
    # Recommended when nr of variables is large.
    PvPartition2 <- CreatePartition(pvals, decreasing=FALSE,uniform=FALSE,ngroup=5,mingr=10)

    #EXAMPLE 4: partition based on subset of variables,
    #e.g. p-values only available for 50 genes.
    genset <- sapply(1:100,function(x) paste("Gene",x))

    subsetgenes <- sort(sapply(sample(1:100,50),function(x) paste("Gene",x)))

    pvals50 <- rbeta(50,1,6)

    #Returns the partition for the subset based on the indices of
    #the variables in entire genset. Variables not
    #present in subset will receive group-penalty = 1 for this partition.

    PvPartitionSubset <- CreatePartition(pvals50, varnamesdata = genset,subset = subsetgenes,
                                         decreasing=FALSE,uniform=TRUE, ngroup=5)

    #EXAMPLE 5: COMBINING PARTITIONS

    #Combines partitions into one list with named components.
    #This can be use as input for the grridge() #function.
    #NOTE: if one aims to use one partition only, then this can be directly used in grridge().

    MyPart <- list(signature=SignaturePartition, type = TypePartition,
                   pval = PvPartition, pvalsubset=PvPartitionSubset)

[Package GRridge version 1.10.0 Index]