get_signatures-DownSamplingConsensusPartition-method: Get signature rows

In cola: A Framework for Consensus Partitioning

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)

cola documentation built on Nov. 8, 2020, 8:12 p.m.