consensus_partition_by_down_sampling: Consensus partitioning only with a subset of columns

In jokergoo/cola: A Framework for Consensus Partitioning

Consensus partitioning only with a subset of columns

Description

Consensus partitioning only with a subset of columns

Usage

consensus_partition_by_down_sampling(data,
    top_value_method = "ATC",
    top_n = NULL,
    partition_method = "skmeans",
    max_k = 6, k = NULL,
    subset = min(round(ncol(data)*0.2), 250), pre_select = TRUE,
    verbose = TRUE, prefix = "", anno = NULL, anno_col = NULL,
    predict_method = "centroid",
    dist_method = c("euclidean", "correlation", "cosine"),
    .env = NULL, .predict = TRUE, mc.cores = 1, cores = mc.cores, ...)

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_methods 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. If top_n is a vector, paritition will be applied to every values in top_n and consensus partition is summarized from all partitions.
partition_method	A single partitioning method. Available methods are in all_partition_methods. Use register_partition_methods to add a new partition method.
max_k	Maximal number of subgroups to try. The function will try for 2:max_k subgroups
k	Alternatively, you can specify a vector k.
subset	Number of columns to randomly sample, or a vector of selected indices.
pre_select	Whether to pre-select by k-means.
verbose	Whether to print messages.
prefix	Internally used.
anno	Annotation data frame.
anno_col	Annotation colors.
predict_method	Method for predicting class labels. Possible values are "centroid", "svm" and "randomForest".
dist_method	Method for predict the class for other columns.
.env	An environment, internally used.
.predict	Internally used.
mc.cores	Number of cores. This argument will be removed in future versions.
cores	Number of cores, or a cluster object returned by makeCluster.
...	All pass to consensus_partition.

Details

The function performs consensus partitioning only with a small subset of columns and the class of other columns are predicted by predict_classes,ConsensusPartition-method.

Examples

## Not run: 
data(golub_cola)
m = get_matrix(golub_cola)

set.seed(123)
golub_cola_ds = consensus_partition_by_down_sampling(m, subset = 50,
	anno = get_anno(golub_cola), anno_col = get_anno_col(golub_cola),
	top_value_method = "SD", partition_method = "kmeans")

## End(Not run)

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