golub_cola: Example ConsensusPartitionList object from Golub dataset
In jokergoo/cola: A Framework for Consensus Partitioning

golub_cola

R Documentation

Example ConsensusPartitionList object from Golub dataset

Description

Example ConsensusPartitionList object from Golub dataset

Usage

data(golub_cola)

Details

Following code was used to generate golub_cola:

    library(cola)

    library(golubEsets)  # from bioc
    data(Golub_Merge)
    m = exprs(Golub_Merge)
    colnames(m) = paste0("sample_", colnames(m))
    anno = pData(Golub_Merge)

    m[m <= 1] = NA
    m = log10(m)

    m = adjust_matrix(m)

    library(preprocessCore)  # from bioc
    cn = colnames(m)
    rn = rownames(m)
    m = normalize.quantiles(m)
    colnames(m) = cn
    rownames(m) = rn

    set.seed(123)
    golub_cola = run_all_consensus_partition_methods(
        m, cores = 6, 
        anno = anno[, c("ALL.AML"), drop = FALSE],
        anno_col = c("ALL" = "red", "AML" = "blue")
    )