aIc.perturb {aIc} R Documentation

## aIc.perturb calculates the perturbation invariance of distance for samples with a given correction. This compares the distances of samples of the full dataset and a the perturbed dataset. This is expected to be true if the transform is behaving rationally in compositional datasets.

### Description

aIc.perturb calculates the perturbation invariance of distance for samples with a given correction. This compares the distances of samples of the full dataset and a the perturbed dataset. This is expected to be true if the transform is behaving rationally in compositional datasets.

### Usage

aIc.perturb(
data,
norm.method = "prop",
zero.remove = 0.95,
zero.method = "prior",
distance = "euclidian",
log = FALSE,
group = NULL
)


### Arguments

 data can be any dataframe or matrix with samples by column norm.method can be prop, clr, RLE, TMM, TMMwsp zero.remove is a value. Filter data to remove features that are 0 across at least that proportion of samples: default 0.95 zero.method can be any of NULL, prior, GBM or CZM. NULL will not impute or change 0 values, GBM (preferred) and CZM are from the zCompositions R package, and prior will simply add 0.5 to all counts. distance can be euclidian, bray, or jaccard. euclidian on log-ratio transformed data is the same as the Aitchison distance. default=euclidian log is a logical. log transform the RLE or TMM outputs, default=FALSE group is a vector containing group information. Required for clr, RLE, TMM, lvha, and iqlr based normalizations.

### Value

Returns a list with the maximum proportional perturbation in ol (expect 0, but values up to 1 is.perturb, the table of distances for the whole and perturbaton in dist.all and dist.perturb, the histogram of the perturbations in plot, and the plot and axis labels in main xlab and ylab. .

Greg Gloor

### Examples

data(selex)
group = c(rep('N', 7), rep('S', 7))
x <- aIc.perturb(selex, group=group, norm.method='clr', distance='euclidian', zero.method='prior')
plot(x$plot, main=x$main, ylab=x$ylab, xlab=x$xlab)


[Package aIc version 1.0 Index]