dispFuncs: Gamma regression parameters describing the mean-dispersion...

In metaRNASeq: Meta-Analysis of RNA-Seq Data

Description

Gamma regression parameters describing the mean-dispersion relationship for each of the two real datasets considered in the associated paper, as estimated using the DESeq package version 1.8.3 (Anders and Huber, 2010).

Usage

data(dispFuncs)

Format

List of length 2, where each list is a vector containing the two estimated coefficients (α_0 and α_1) for the gamma regression in each study (see details below).

Details

The dispFuncs object contains the estimated coefficients from the parametric gamma regressions describing the mean-dispersion relationship for the two real datasets considered in the associated paper. The gamma regressions were estimated using the DESeq package version 1.8.3 (Anders and Huber, 2010).

Briefly, after estimating a per-gene mean expression and dispersion values, the DESeq package fits a curve through these estimates. These fitted values correspond to an estimation of the typical relationship between mean expression values μ and dispersions α within a given dataset. By default, this relationship is estimated using a gamma-family generalized linear model (GLM), where two coefficients α_0 and α_1 are found to parameterize the fit as α = α_0 + α_1 / μ.

For the first dataset (F078), the estimated mean-dispersion relationship is described using the following gamma-family GLM:

α = 0.024 + 14.896 / μ.

For the second dataset (F088), the estimated mean-dispersion relationship is described using the following gamma-family GLM:

α = 0.00557 + 1.54247 / μ.

These gamma-family GLMs describing the mean-dispersions relationship in each of the two datasets are used in this package to simulate data using dispersion parameters that are as realistic as possible.

References

A. Rau, G. Marot and F. Jaffrezic (2014). Differential meta-analysis of RNA-seq data. BMC Bioinformatics 15:91

S. Anders and W. Huber (2010). Differential expression analysis for sequence count data. Genome Biology, 11:R106.

See Also

sim.function

Examples

data(dispFuncs)

Example output

metaRNASeq documentation built on Sept. 30, 2021, 3 p.m.