combiningMappings {STATegRa} | R Documentation

## combiningMappings, combining several mappings for use in the omicsNPC function

### Description

This function combines several annotation so that measurements across different datasets are mapped to the same reference elements (e.g., genes). The annotations should all be either data frame / matrices, named vectors/lists, or bioMap objects. See the examples for further details

### Usage

    combiningMappings(mappings, reference = NULL, retainAll = FALSE)

### Arguments

`mappings` | List of annotations.
`reference` | If the annotations are data frame, matrices or bioMap objects, the name of the column containing the reference elements
`retainAll` | Logical, if set to TRUE measurements that have no counterparts in other datasets are retained

### Value

A data frame encoding the mapping across several dataset

### Author(s)

Vincenzo Lagani

### References

Nestoras Karathanasis, Ioannis Tsamardinos and Vincenzo Lagani. omicsNPC: applying the Non-Parametric Combination methodology to the integrative analysis of heterogeneous omics data. Submitted to PlosONE.

### Examples

    #Example 1
    #Mapping with data frames
    mRNA <- data.frame(gene = rep(c('G1', 'G2', 'G3'), each = 2), probeset = paste('p', 1:6, sep = ''));
    methylation <- data.frame(gene = c(rep('G1', 3), rep('G2', 4)),
                                     methy = paste('methy', 1:7, sep = ''));
    miRNA <- data.frame(gene = c(rep('G1', 2), rep('G2', 1), rep('G3', 2)),
                                   miR = c('miR1', 'miR2', 'miR1', 'miR1', 'miR2'));
    mappings <- list(mRNA = mRNA, methylation = methylation, miRNA = miRNA);
    combiningMappings(mappings = mappings, retainAll = TRUE)

    #Example 2
    #Mapping with character vectors
    mRNA <- rep(c('G1', 'G2', 'G3'), each = 2);
    names(mRNA) = paste('p', 1:6, sep = '');
    methylation <- c(rep('G1', 3), rep('G2', 4));
    names(methylation) = paste('methy', 1:7, sep = '');
    miRNA <- c(rep('G1', 2), rep('G2', 1), rep('G3', 2));
    names(miRNA) = c('miR1', 'miR2', 'miR1', 'miR1', 'miR2');
    mappings <- list(mRNA = mRNA, methylation = methylation, miRNA = miRNA);
    combiningMappings(mappings = mappings, retainAll = TRUE)

[Package STATegRa version 1.20.0 Index]