meanVarParaFit {MAnorm2} | R Documentation |
Parametrically Fit a Mean-Variance Curve
Description
meanVarParaFit
fits a mean-variance curve by applying a robust,
gamma-family glm
regression, taking advantage of the
form: var = c1 + c2 / (2 ^ mean)
.
Usage
meanVarParaFit(
x,
y,
weight,
range.residual = c(1e-04, 15),
max.iter = 50,
init.coef = NULL,
verbose = TRUE
)
Arguments
x |
Two numeric vectors of (sample) means and sample variances, respectively. |
y |
Two numeric vectors of (sample) means and sample variances, respectively. |
weight |
An optional vector of weights to be used in the fitting
procedure. It's typically used when sample variances in |
range.residual |
A length-two vector specifying the range of residuals of non-outliers. |
max.iter |
Maximum number of iteration times allowed during the fitting procedure. |
init.coef |
An optional length-two vector specifying the initial values of the coefficients. |
verbose |
Whether to print processing messages about iteratively fitting the mean-variance curve? |
Details
meanVarParaFit
iteratively detects outliers and fits a generalized
linear model on non-outliers. The procedure converges as soon as the set of
outlier points fixes.
See "References" for the theoretical foundation of the parametric form.
Value
A prediction function which accepts a vector of means and returns
the predicted variances, with an attribute named "coefficients"
attached.
References
Robinson, M.D. and G.K. Smyth, Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 2008. 9(2): p. 321-32.
Love, M.I., W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014. 15(12): p. 550.
Tu, S., et al., MAnorm2 for quantitatively comparing groups of ChIP-seq samples. Genome Res, 2021. 31(1): p. 131-145.
See Also
meanVarLocalFit
for using local regression to fit
a mean-variance curve; fitMeanVarCurve
for an interface
to modeling the mean-variance dependence on bioCond
objects; plotMeanVarCurve
for plotting a mean-variance
curve.