Mergeomics (version 1.0.0)

tool.aggregate: 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

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

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