model.nbs.m: Modeling NBS Genewise Dispersion with the Maximum Ajdusted...
In gu-mi/NBGOF: Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data
Description
Usage
Arguments
Details
Value
Author(s)
References
Description
This function fits an NBS dispersion model where the dispersion is modeled as a smooth function
(a natural cubic spline function) of the preliminary estimates of the log mean realtive frequencies.
The output of this function will be passed to the main GOF function nb.gof.m.
Usage
1
model.nbs.m(counts, x, lib.sizes=colSums(counts), method=method)
Arguments
counts
an m-by-n count matrix of non-negative integers. For a typical
RNA-Seq experiment, this is the read counts with m genes and n samples.
x
an n-by-p design matrix.
lib.sizes
library sizes of an RNA-Seq experiment. Default is the column
sums of the counts matrix.
method
method for estimating dispersions.
Details
See the estimate.dispersion function in the NBPSeq package
for more information.
Value
A list of quantities to be used in the main nb.gof.m function.
Author(s)
Gu Mi <neo.migu@gmail.com>, Yanming Di, Daniel Schafer
References
Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial
Model for Assessing Differential Gene Expression from RNA-Seq", Statistical
Applications in Genetics and Molecular Biology, 10 (1).
See https://github.com/gu-mi/NBGOF/wiki/ for more details.
gu-mi/NBGOF documentation built on Oct. 25, 2020, 3:30 a.m.
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Description Usage Arguments Details Value Author(s) References
Description
This function fits an NBS dispersion model where the dispersion is modeled as a smooth function
(a natural cubic spline function) of the preliminary estimates of the log mean realtive frequencies.
The output of this function will be passed to the main GOF function nb.gof.m.
Usage
1 | model.nbs.m(counts, x, lib.sizes=colSums(counts), method=method)
|
Arguments
counts |
an m-by-n count matrix of non-negative integers. For a typical RNA-Seq experiment, this is the read counts with m genes and n samples. |
x |
an n-by-p design matrix. |
lib.sizes |
library sizes of an RNA-Seq experiment. Default is the column
sums of the |
method |
method for estimating dispersions. |
Details
See the estimate.dispersion function in the NBPSeq package
for more information.
Value
A list of quantities to be used in the main nb.gof.m function.
Author(s)
Gu Mi <neo.migu@gmail.com>, Yanming Di, Daniel Schafer
References
Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq", Statistical Applications in Genetics and Molecular Biology, 10 (1).
See https://github.com/gu-mi/NBGOF/wiki/ for more details.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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