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.`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.

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

`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. |

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

```
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]