R: Transformations

Transformations {GiANT} | R Documentation

## Transformations

### Description

Functions to transform the gene-level statistic values prior to the calculation of the gene set statistics, as used in the `transformation` parameter of `gsAnalysis`. Most of the functions wrap existing R functions.

### Usage

    transformation.abs(x)

    transformation.square(x)

    transformation.localFdr(x,
    	statistic="pvalue",
    	cutoff.method="fndr",
    	pct0=0.75)

    transformation.binarize(x, quant)

    transformation.rank(x)

    transformation.adjust(x, adjMethod = "fdr")

    transformation.adjustAndBinarize(x, adjMethod = "fdr", threshold = 0.05)

### Arguments

`x` | A numeric vector of gene-level statistic values, one per gene. These values are calculated by the previous step (see `gls`).
`statistic` | Specifies the null model for `transformation.localFdr` (see `statistic` parameter of `fdrtool` for possible values).
`cutoff.method` | Type of cut-off method used in `transformation.localFdr` (see `cutoff.method` parameter of `fdrtool` for possible values).
`pct0` | Fraction of data used by `transformation.localFdr` if `cutoff.method="pct0"` (see `fdrtool` for a detailed description).
`quant` | For `transformation.binarize`, this numeric value in the interval [0,1] defines the percentage of gene-level statistic values which should be set to zero. The remaining values are set to one.
`adjMethod` | The method to use for the adjustment for multiple testing (see `method` parameter of `p.adjust` for possible values).
`threshold` | The threshold for differential expression of a gene (defaults to `0.05`). Values smaller than these threshold are set to 1 , others to 0.

### Details

Standard transformation functions for gene-level statistics (to be used in an analysis pipeline defined by `gsAnalysis`):

- `transformation.abs`: Calculates the absolute values of the elements in `x` (a wrapper for `abs`).

- `transformation.square`: Squares all elements in `x`.

- `transformation.localFdr`: Calculates the local fdr for the elements in `x`. This is a wrapper for `fdrtool`.

- `transformation.binarize`: Binarizes the values in `x` by using the `quant` quantile as a threshold.

- `transformation.rank`: Ranks the values in `x` and returns the rank vector.

- `transformation.adjust`: Adjusts for multiple testing according to the adjustment method specified in `adjMethod`.

- `transformation.adjustAndBinarize`: Adjusts for multiple testing according to the adjustment method specified in `adjMethod` and binarizes the resulting p-values according to `threshold` (values smaller than the threshold become 1 others 0).

### Value

All functions return a vector of transformed values having the same length as `x`.

### See Also

`geneSetAnalysis`, `gsAnalysis`, `gss`, `gls`

[Package GiANT version 1.2 Index]