tool.aggregate {Mergeomics} | R Documentation

## Aggregate the entries

### Description

`tool.aggregate` aggregates the entries with respect to the given feature. It first finds raw indices (either genes or markers), then sorts them, and finds the blocks (segments) of identical entries.

### Usage

    tool.aggregate(entries, limit = 1)

### Arguments

`entries` | an array that will be sorted and aggregated within blocks
`limit` | minimum block size to be included

### Value

`res` | a data list with the following components:
    labels: shared values within blocks
    lengths: numbers of entries in blocks
    blocks: integer arrays of entry positions within blocks
    ranks: entry positions included in blocks

### Author(s)

Ville-Petteri Makinen

### References

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

### Examples

    aa <- data.frame(MODULE=c("Mod1", "Mod1", "Mod2", "Mod2", "Mod3"),
    GENE=c("GeneA", "GeneC", "GeneB", "GeneC", "GeneA"))
    ## aggregate according to the module names:
    bb <- tool.aggregate(aa$MODULE)
    bb
    ## aggregate according to the gene names:
    cc <- tool.aggregate(aa$GENE)
    cc

[Package Mergeomics version 1.10.0 Index]