OVESEGtstat: OVESEG-test statistics

In OVESEG: OVESEG-test to detect tissue/cell-specific markers

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)

OVESEG documentation built on Nov. 8, 2020, 4:51 p.m.