get_signatures-HierarchicalPartition-method: Get signatures rows

In jokergoo/cola: A Framework for Consensus Partitioning

Get signatures rows

Description

Get signatures rows

Usage

## S4 method for signature 'HierarchicalPartition'
get_signatures(object, merge_node = merge_node_param(),
    group_diff = object@param$group_diff,
    row_km = NULL, diff_method = "Ftest", fdr_cutoff = object@param$fdr_cutoff,
    scale_rows = object[1]@scale_rows,
    anno = get_anno(object),
    anno_col = get_anno_col(object),
    show_column_names = FALSE, column_names_gp = gpar(fontsize = 8),
    verbose = TRUE, plot = TRUE, seed = 888,
    ...)

Arguments

object	a HierarchicalPartition-class object.
merge_node	Parameters to merge sub-dendrograms, see merge_node_param.
group_diff	Cutoff for the maximal difference between group means.
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.
fdr_cutoff	Cutoff for FDR of the difference test between subgroups.
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.
column_names_gp	Graphic parameters for column names.
verbose	whether to print messages.
plot	whether to make the plot.
seed	Random seed.
...	other arguments pass to get_signatures,ConsensusPartition-method.

Details

The function calls get_signatures,ConsensusPartition-method to find signatures at each node of the partition hierarchy.

Value

A data frame with more than two columns:

which_row:

row index corresponding to the original matrix.

km:

the k-means groups if row_km is set.

other_columns:

the mean value (depending rows are scaled or not) in each subgroup.

Author(s)

Zuguang Gu <[e-mail]>

Examples

data(golub_cola_rh)
tb = get_signatures(golub_cola_rh)
head(tb)

jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.