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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
r-bioc-dexseq-1.36.0+dfsg/inst/doc/DEXSeq.Rmd-625-This model is fit separately for each counting bin $i$. The coefficient $\beta^\text{S}_{ij}$ accounts for the sample-specific contribution (factor `sample`), the term $\beta^\text{E}_{i}$
r-bioc-dexseq-1.36.0+dfsg/inst/doc/DEXSeq.Rmd:626:is only included if $l=1$ and hence estimates the logarithm of the ratio $K_{ij1}/K_{ij0}$ between the counts for all other exons and the counts for the tested exon. As this coefficient is estimated from data from all samples, it can be considered as a measure of "average exon usage". In the R model formula, it is represented by the term `exon` with its two levels `this` ($l=0$) and `others` ($l=1$). Finally, the last term, $\beta^\text{EC}_{i,\rho_j}$, captures the interaction `condition:exon`, i.e., the change in exon usage if sample $j$ is from experimental condition group $\rho(j)$. Here, the first condition, $\rho=0$, is absorbed in the sample coefficients, i.e., $\beta^\text{EC}_{i0}$ is fixed to zero and does not appear in the model matrix.
r-bioc-dexseq-1.36.0+dfsg/inst/doc/DEXSeq.Rmd-627-
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r-bioc-dexseq-1.36.0+dfsg/vignettes/DEXSeq.Rmd-625-This model is fit separately for each counting bin $i$. The coefficient $\beta^\text{S}_{ij}$ accounts for the sample-specific contribution (factor `sample`), the term $\beta^\text{E}_{i}$
r-bioc-dexseq-1.36.0+dfsg/vignettes/DEXSeq.Rmd:626:is only included if $l=1$ and hence estimates the logarithm of the ratio $K_{ij1}/K_{ij0}$ between the counts for all other exons and the counts for the tested exon. As this coefficient is estimated from data from all samples, it can be considered as a measure of "average exon usage". In the R model formula, it is represented by the term `exon` with its two levels `this` ($l=0$) and `others` ($l=1$). Finally, the last term, $\beta^\text{EC}_{i,\rho_j}$, captures the interaction `condition:exon`, i.e., the change in exon usage if sample $j$ is from experimental condition group $\rho(j)$. Here, the first condition, $\rho=0$, is absorbed in the sample coefficients, i.e., $\beta^\text{EC}_{i0}$ is fixed to zero and does not appear in the model matrix.
r-bioc-dexseq-1.36.0+dfsg/vignettes/DEXSeq.Rmd-627-