combiningMappings: combiningMappings, combining several mappings for use in the...

In llrs/STATegRa: Classes and methods for multi-omics data integration

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)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.