OVESEGtstat {OVESEG} | R Documentation

## OVESEG-test statistics

### Description

This function computes OVESEG-test statistics.

### Usage

    OVESEGtstat(y, group, weights = NULL, alpha = "moderated",
      order.return = FALSE, lmfit.return = FALSE)

### Arguments

`y` | a numeric matrix containing log-expression or logCPM (log2-counts per million) values. Data frame or SummarizedExperiment object will be internally coerced into a matrix. Rows correspond to probes and columns to samples. Missing values are not permitted.
`group` | categorical vector or factor giving group membership of columns of y. At least two categories need to be presented.
`weights` | optional numeric matrix containing prior weights for each spot.
`alpha` | parameter specifying within-group variance estimator to be used. 'moderated': empirical Bayes moderated variance estimator as used in `eBayes`. Numeric value: a constant value added to pooled variance estimator (α + σ). NULL: no estimator; all variances are set to be 1.
`order.return` | a logical indicating whether the order of groups will be returned. If FALSE, only the highest expressed group index is return for each probe.
`lmfit.return` | a logical indicating whether a `MArrayLM` fitted model object produced by `lmFit` should be returned.

### Details

OVESEG-test statistics are designed to mathematically match the definition of molecular markers:

\max_{k=1,...,K}≤ft\{min_{l \neq k}≤ft\{ \frac{μ_k(j)-μ_l(j)} {σ(j)√{\frac{1}{N_k}+\frac{1}{N_l}}} \right\}\right\}

where j is probe index, K is the number of groups, and μ_k is the mean expression of group k.

### Value

a list containing the following components:

`tstat` | a vector of OVESEG-test statistics for probes.
`label` | a vector of group labels.
`groupOrder` | If `order.return` is TRUE, a matrix with each row being group indexes ordered based on decreasing expression levels. If `order.return` is FALSE, a vector with each element being a probe's highest expressed group index. Group indexes are positions in `label`.
`fit` | a `MArrayLM` fitted model object produced by `lmFit`. Returned only when `lmfit.return` is TRUE.

### Examples

    data(RocheBT)
    rtstat <- OVESEGtstat(RocheBT$y, RocheBT$group, alpha='moderated')
    rtstat <- OVESEGtstat(RocheBT$y, RocheBT$group, alpha=0.1)

[Package OVESEG version 1.3.0 Index]