consensus_partition: Consensus partition

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/consensus_partition.R View source: R/consensus_partition.R

Description

Consensus partition

Usage

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consensus_partition(data,
    top_value_method = "MAD",
    top_n = seq(min(1000, round(nrow(data)*0.1)),
    min(5000, round(nrow(data)*0.5)),
    length.out = 5),
    partition_method = "kmeans",
    max_k = 6,
    p_sampling = 0.8,
    partition_repeat = 50,
    partition_param = list(),
    anno = NULL,
    anno_col = NULL,
    scale_rows = NULL,
    verbose = TRUE,
    .env = NULL)

Arguments

data

a numeric matrix where subgroups are found by columns.

top_value_method

a single top value method. Available methods are in all_top_value_methods. Use register_top_value_method to add a new top value method.

top_n

number of rows with top values. The value can be a vector with length > 1. When n > 5000, the function only randomly sample 5000 rows from top n rows.

partition_method

a single partition method. Available methods are in all_partition_methods. Use register_partition_method to add a new partition method.

max_k

maximum number of partitions to try. The function will try 2:max_k partitions.

p_sampling

proportion of the top n rows to sample.

partition_repeat

number of repeats for the random sampling.

partition_param

parameters for the partition method which are passed to ... in a registered partition method. See register_partition_method for detail.

anno

a data frame with known annotation of samples. The annotations will be plotted in heatmaps and the correlation to predicted subgroups will be tested.

anno_col

a list of colors (a named vector) for the annotations in anno. If not specified, random colors are used.

scale_rows

whether to scale rows. If it is TRUE, scaling method defined in register_partition_method is used.

verbose

whether print messages.

.env

an environment, internally used.

Details

The function performs analysis in following steps:

Value

A ConsensusPartition-class object. Simply type the name of the object in the R interactive session to see which functions can be applied on it.

Author(s)

Zuguang Gu <[email protected]>

See Also

run_all_consensus_partition_methods runs consensus partition with multiple top value methods and multiple partition methods. hierarchical_partition runs consensus partition hierarchically.

Examples

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# There is no example
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jokergoo/cola documentation built on June 27, 2018, 10:35 a.m.