subtype_pins: Subtypes using PINSPlus package

Description Usage Arguments Details Value See Also

Description

Perform subtyping using multiple types of data

Usage

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subtype_pins(data_list, minimal_return = FALSE, return_stage_2 = TRUE,
  k_max = 5, agreement_cutoff = 0.5, verbose = T, ...)

Arguments

data_list

a list of data matrices with continuous data of format samples x features (with the same number of samples).

minimal_return

logical, if TRUE, the result of the function will just be what's needed to evaluate the goodness of the partition, i.e. the partition and the element for internal metrics.

return_stage_2

logical to return the partition of the stage 2 of the PINS method's workflow.

k_max

The maximum number of clusters tested (from 2 to k_max). Default value is 5.

agreement_cutoff

Agreement threshold to be considered consistent. Default value is 0.5.

verbose

Set it to TRUE of FALSE to get more or less details respectively.

...

these arguments will be passed to PerturbationClustering algorithm. See PerturbationClustering.

Details

subtype_pins uses SubtypingOmicsData. The input is a list of data matrices where each matrix represents the molecular measurements of a data type. The input matrices must have the same number of rows. The function aims to find the optimum number of subtypes and location of each sample in the clusters from integrated input data dataList through two processing stages:

Value

a result list containing:

See Also

PerturbationClustering, SubtypingOmicsData.


agapow/subtypr documentation built on May 5, 2019, 1:33 a.m.