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

Description Usage Arguments Value Author(s) References Examples

View source: R/STATegRa_combiningMappings.R

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

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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

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#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.