Bagged.RDA.Feature.Selection: Description: BAGGED RDA feature selection

Description Usage Arguments Value Author(s) References Examples

View source: R/rda.R

Description

Arguments:

Usage

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Bagged.RDA.Feature.Selection(X, Y, sig.thresh = 0.1, nboot = 1000,
  verbose = T)

Arguments

X

a matrix, samples on columns, variables (bacteria) on rows.

Y

vector with names(Y)=rownames(X), for example

sig.thresh

signal p-value threshold, default 0.1

nboot

Number of bootstrap iterations

verbose

verbose

Returns:

Value

List with items: loadings: bagged loadings scores: bagged scores significance: significances of X variables group.centers: group centers on latent space bootstrapped: bootstrapped loadings data: data set with non-significant components dropped out.

Author(s)

Contact: Jarkko Salojarvi [email protected]

References

See citation("microbiome")

Examples

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#
#  library(microbiome)
#  data(peerj32)
#  x <- t(peerj32$microbes)
#  y <- factor(peerj32$meta$time); names(y) <- rownames(peerj32$meta)
# Bag.res <- Bagged.RDA.Feature.Selection(x, y, sig.thresh=0.05, nboot=100)
# PlotBaggedRDA(Bag.res, y)

microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.