golub_cola {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, mc.cores = 2,
            anno = anno[, c("ALL.AML"), drop = FALSE],
            anno_col = c("ALL" = "red", "AML" = "blue")
        )

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### See Also

https://jokergoo.github.io/cola_examples/Golub_leukemia/

### Examples

    data(golub_cola)
    golub_cola

[Package cola version 1.6.0 Index]