get_signatures-HierarchicalPartition-method {cola}R Documentation

Get signatures rows

Description

Get signatures rows

Usage

## S4 method for signature 'HierarchicalPartition'
get_signatures(object, depth = max_depth(object),
    scale_rows = object[1]@scale_rows,
    anno = get_anno(object),
    anno_col = get_anno_col(object),
    show_column_names = FALSE,
    verbose = TRUE, plot = TRUE,
    silhouette_cutoff = 0.5,
    ...)

Arguments

object

A HierarchicalPartition-class object.

depth

Depth of the hierarchy.

scale_rows

Whether apply row scaling when making the heatmap.

anno

A data frame of annotations for the original matrix columns. By default it uses the annotations specified in hierarchical_partition.

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.

show_column_names

Whether show column names in the heatmap.

verbose

Whether to print messages.

plot

Whether to make the plot.

silhouette_cutoff

Cutoff for silhouette scores. Samples with values less than it are not used for finding signature rows. For selecting a proper silhouette cutoff, please refer to https://www.stat.berkeley.edu/~s133/Cluster2a.html#tth_tAb1.

...

Other arguments

Details

The function calls get_signatures,ConsensusPartition-method to find signatures at each node of the partition hierarchy. The final signatures are the union of all signatures at all nodes.

Value

A list of row indices where rows are significantly different between subgroups in at least one node. Other columns in the returned data frames are whether the rows are significantly different in the node.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

## Not run: 
data(cola_rh)
get_signatures(cola_rh)

## End(Not run)

[Package cola version 1.0.1 Index]