get_signatures-DownSamplingConsensusPartition-method {cola} | R Documentation

## Get signature rows

### Description

Get signature rows

### Usage

    ## S4 method for signature 'DownSamplingConsensusPartition'
    get_signatures(object, k,
        p_cutoff = 0.05,
        fdr_cutoff = cola_opt$fdr_cutoff,
        group_diff = cola_opt$group_diff,
        scale_rows = object@scale_rows,
        row_km = NULL,
        diff_method = c("Ftest", "ttest", "samr", "pamr", "one_vs_others"),
        anno = get_anno(object),
        anno_col = get_anno_col(object),
        internal = FALSE,
        show_row_dend = FALSE,
        show_column_names = FALSE, use_raster = TRUE,
        plot = TRUE, verbose = TRUE, seed = 888,
        left_annotation = NULL, right_annotation = NULL,
        col = if(scale_rows) c("green", "white", "red") else c("blue", "white", "red"),
        simplify = FALSE,
        ...)

### Arguments

`object` | A `DownSamplingConsensusPartition-class` object.
`k` | Number of subgroups.
`p_cutoff` | Cutoff for p-values of class label prediction. Samples with values higher than it are not used for finding signature rows.
`fdr_cutoff` | Cutoff for FDR of the difference test between subgroups.
`group_diff` | Cutoff for the maximal difference between group means.
`scale_rows` | Whether apply row scaling when making the heatmap.
`row_km` | Number of groups for performing k-means clustering on rows. By default it is automatically selected.
`diff_method` | Methods to get rows which are significantly different between subgroups, see 'Details' section.
`anno` | A data frame of annotations for the original matrix columns. By default it uses the annotations specified in `consensus_partition` or `run_all_consensus_partition_methods`.
`anno_col` | A list of colors (color is defined as a named vector) for the annotations. If `anno` is a data frame, `anno_col` should be a named list where names correspond to the column names in `anno`.
`internal` | Used internally.
`show_row_dend` | Whether show row dendrogram.
`show_column_names` | Whether show column names in the heatmap.
`use_raster` | Internally used.
`plot` | Whether to make the plot.
`verbose` | Whether to print messages.
`seed` | Random seed.
`left_annotation` | Annotation put on the left of the heatmap. It should be a `HeatmapAnnotation-class` object. The number of items should be the same as the number of the original matrix rows. The subsetting to the significant rows are automatically performed on the annotation object.
`right_annotation` | Annotation put on the right of the heatmap. Same format as `left_annotation`.
`col` | Colors.
`simplify` | Only use internally.
`...` | Other arguments.

### Details

This function is very similar as `get_signatures,ConsensusPartition-method`.

### Examples

    data(golub_cola_ds)
    get_signatures(golub_cola_ds, k = 2)
    get_signatures(golub_cola_ds, k = 3)

[Package cola version 1.6.0 Index]