estimateGLMTrendedDisp {edgeR} | R Documentation |
Estimates the dispersion parameter for each transcript (tag) with a trend that depends on the overall level of expression for the transcript for a DGE dataset for general experimental designs by using Cox-Reid approximate conditional inference for a negative binomial generalized linear model for each transcript (tag) with the unadjusted counts and design matrix provided.
## S3 method for class 'DGEList' estimateGLMTrendedDisp(y, design, offset=NULL, method="bin.spline", ...) ## Default S3 method: estimateGLMTrendedDisp(y, design, offset=NULL, method="bin.spline", ...)
y |
an object that contains the raw counts for each library (the measure of expression level); it can either be a matrix of counts, or a |
design |
numeric matrix giving the design matrix for the GLM that is to be fit. |
method |
method (low-level function) used to estimated the trended dispersions.
Possible values are |
offset |
numeric scalar, vector or matrix giving the offset (in addition to the log of the effective library size) that is to be included in the NB GLM for the transcripts. If a scalar, then this value will be used as an offset for all transcripts and libraries. If a vector, it should be have length equal to the number of libraries, and the same vector of offsets will be used for each transcript. If a matrix, then each library for each transcript can have a unique offset, if desired. In |
... |
other arguments are passed to lower-level functions.
See |
This is a wrapper function for the lower-level functions that actually carry out the dispersion estimation calculations. Provide a convenient, object-oriented interface for users.
When the input object is a DGEList
, estimateGLMTrendedDisp
produces a DGEList
object, which contains the estimates of the trended dispersion parameter for the negative binomial model according to the method applied.
When the input object is a numeric matrix, the output of one of the lower-level functions dispBinTrend
, dispCoxReidPowerTrend
of dispCoxReidSplineTrend
is returned.
Gordon Smyth, Davis McCarthy
Cox, DR, and Reid, N (1987). Parameter orthogonality and approximate conditional inference. Journal of the Royal Statistical Society Series B 49, 1-39.
dispBinTrend
, dispCoxReidPowerTrend
and dispCoxReidSplineTrend
for details on how the calculations are done.
estimateGLMCommonDisp
for common dispersion and estimateGLMTagwiseDisp
for (trended) tagwise dispersion in the context of generalized linear models.
estimateCommonDisp
for common dispersion or estimateTagwiseDisp
for tagwise dispersion in the context of a multiple group experiment (one-way layout).
y <- matrix(rnbinom(1000,mu=10,size=10),ncol=4) d <- DGEList(counts=y,group=c(1,1,2,2),lib.size=c(1000:1003)) design <- model.matrix(~group, data=d$samples) # Define the design matrix for the full model disp <- estimateGLMTrendedDisp(d, design, min.n=10)