dmSQTLfit-class


dmSQTLfit extends the <code>dmDSdispersion</code> class by adding the
full model Dirichlet-multinomial feature proportion estimates needed for the
sQTL analysis. Feature ratios are estimated for each gene and each group that
is defined by different SNPs/blocks. Result of <code><a rd-options="" href="/link/dmFit?package=DRIMSeq&version=1.0.2" data-mini-rdoc="DRIMSeq::dmFit">dmFit</a></code>.


The package provides two frameworks. One for the differential
splicing analysis between different conditions and one for the sQTL analysis.
Both are based on modeling the counts of genomic features (i.e., transcripts,
exons or exonic bins) with Dirichlet-multinomial distribution. The package also
makes available functions for visualization and exploration of the data and
results.

Malgorzata Nowicka

DRIMSeq

Differential splicing and sQTL analyses with Dirichlet-multinomial model
in RNA-Seq

dmSQTLfit-class function

 <dl>
<dt><code>dispersion</code></dt><dd>Character specifying which type of dispersion was used for
fitting: <code>"common_dispersion"</code> or <code>"genewise_dispersion"</code>.</dd> <dt><code>fit_full</code></dt><dd>List of <code>MatrixList</code> objects. Each element
of this list contains the full model proportion estimates for all the
blocks associated with a given gene. Columns of MatrixLists correspond to 3
genotypes (0,1,2). The full model likelihoods are stored in <code>metadata</code>
slot.</dd> </dl>

Slots

dmSQTLfit extends the <code><linkS4class>dmDSdispersion</linkS4class></code> class by adding the
full model Dirichlet-multinomial feature proportion estimates needed for the
sQTL analysis. Feature ratios are estimated for each gene and each group that
is defined by different SNPs/blocks. Result of <code><a href="dmFit" rd-options="">dmFit</a></code>.

dmSQTLfit-class: dmSQTLfit object

Description

Arguments

Slots

See Also