run_all_consensus_partition_methods: Consensus partitioning for all combinations of methods

In jokergoo/cola: A Framework for Consensus Partitioning

Consensus partitioning for all combinations of methods

Description

Consensus partitioning for all combinations of methods

Usage

run_all_consensus_partition_methods(data,
    top_value_method = all_top_value_methods(),
    partition_method = all_partition_methods(),
    max_k = 6, k = NULL,
    top_n = NULL,
    mc.cores = 1, cores = mc.cores, anno = NULL, anno_col = NULL,
    sample_by = "row", p_sampling = 0.8, partition_repeat = 50,
    scale_rows = NULL, verbose = TRUE, help = cola_opt$help)

Arguments

data	A numeric matrix where subgroups are found by columns.
top_value_method	Method which are used to extract top n rows. Allowed methods are in all_top_value_methods and can be self-added by register_top_value_methods.
partition_method	Method which are used to partition samples. Allowed methods are in all_partition_methods and can be self-added by register_partition_methods.
max_k	Maximal number of subgroups to try. The function will try 2:max_k subgroups.
k	Alternatively, you can specify a vector k.
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. If top_n is a vector, paritition will be applied to every values in top_n and consensus partition is summarized from all partitions.
mc.cores	Number of cores to use. This argument will be removed in future versions.
cores	Number of cores, or a cluster object returned by makeCluster.
anno	A data frame with known annotation of columns.
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.
sample_by	Should randomly sample the matrix by rows or by columns?
p_sampling	Proportion of the top n rows to sample.
partition_repeat	Number of repeats for the random sampling.
scale_rows	Whether to scale rows. If it is TRUE, scaling method defined in register_partition_methods is used.
verbose	Whether to print messages.
help	Whether to print help messages.

Details

The function performs consensus partitioning by consensus_partition for all combinations of top-value methods and partitioning methods.

It also adjsuts the subgroup labels for all methods and for all k to make them as consistent as possible.

Value

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

Author(s)

Zuguang Gu <[e-mail]>

Examples

## Not run: 
set.seed(123)
m = cbind(rbind(matrix(rnorm(20*20, mean = 1), nr = 20),
                matrix(rnorm(20*20, mean = -1), nr = 20)),
          rbind(matrix(rnorm(20*20, mean = -1), nr = 20),
                matrix(rnorm(20*20, mean = 1), nr = 20))
         ) + matrix(rnorm(40*40), nr = 40)
rl = run_all_consensus_partition_methods(data = m, top_n = c(20, 30, 40))

## End(Not run)

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