Function aggregate_probes aggregates CpG probes to corresponding genes.

aggregate_probes(data, keep = NULL, = MLExpResso::illumina_humanmethylation_27_data,
  genes.col = 11, probes.col = 1)



Data frame containing methylation values for CpG probes. Columns correspond to probes, rows to samples.


The name of the column or vector of columns names we want to keep.

#' @param Data frame which contains information about CpG probes and corresponding genes, by default in our package we use illumina_humanmethylation_27_data. New dataset should contain 5 columns with: 1) CpG probe names, 2) CpG probe locations, 3) gene names, 4) logical value if there is a CpG island, 5) location of island.


Number of column in containing informations about genes (genes symbols).


Number of column in containing informations about probes (probes symbols).


A data frame with CpG probes aggregated to genes. If there were more than one probe corresponding to a gene, value is a mean of those probes.


# NOT RUN { library(MLExpRessoData) BRCA_genes <- aggregate_probes(BRCA_methylation_all, keep="SUBTYPE") # }