bsPAMR: Perform PAMR bootstrapping.

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

Description

Use PAMR algorithm and bootstrapping to derive a robust feature set.

Usage

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bsPAMR(logX, groupings, DIR=NULL, params = NULL)

Arguments

logX

The data matrix.

groupings

The grouping variable.

DIR

The output base directory.

params

A parameter list with the following elements:
seed: A random seed.
bstr: Number of bootstrap iterations. jitter: Boolean. Use some additional noise for constant values. ncv: Number of inner crossvalidation folds. max_allowed_feat: Maximum number of allowed features in the feature set. n.threshold: Threshold parameter for PAMR. saveres: Boolean. Stored results of bootstrapping in an R-data object.

Details

Usually called from doBS.

Value

The result list of the bootstrapping, which is a list: For each classification instance in groupings, one element is saved, each a list with bstr elements, from which each again is a list holding the following elements:

histtr

training object generated with pamr.train.

histcv

cv object generated with pamr.cv

tmin

Minimal threshold value for the feature selection.

selected

Indices of selected features at tmin.

selected_names

Names of selected features at tmin.

To get to one bootstrapping element, one could use for example: returnobject[[1]][[1]][["tmin"]] to get access to the minimal threshold of the first bootstrapping iteration in the first classification problem.

Author(s)

Christian Bender ([email protected])

See Also

doBS

Examples

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## Not run: 
#todo

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bootfs documentation built on May 2, 2019, 5:50 p.m.