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'Benjamini-Hodgberg' to 'Benjamini-Hochberg' #65

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2 changes: 1 addition & 1 deletion vignettes/dNdScv.Rmd
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Expand Up @@ -42,7 +42,7 @@ We have run dNdScv with default parameters. This includes removing ultra-hypermu

#####dndscv outputs: Table of significant genes

The output of the *dndscv* function is a list of objects. For an analysis of exome or genome data, the most relevant output will often be the result of neutrality tests at gene level. *P-values* for substitutions are obtained by Likelihood-Ratio Tests as described in (Martincorena *et al*, 2017) and q-values are obtained by Benjamini-Hodgberg's multiple testing correction. The table also includes information on the number of substitutions of each class observed in each gene, as well as maximum-likelihood estimates (MLEs) of the dN/dS ratios for each gene, for missense (*wmis*), nonsense (*wnon*), essential splice site mutations (*wspl*) and indels (*wind*). The global q-value integrating all mutation types are available in the *qglobal_cv* and *qallsubs_cv* columns for analyses with and without indels, respectively.
The output of the *dndscv* function is a list of objects. For an analysis of exome or genome data, the most relevant output will often be the result of neutrality tests at gene level. *P-values* for substitutions are obtained by Likelihood-Ratio Tests as described in (Martincorena *et al*, 2017) and q-values are obtained by Benjamini-Hochberg's multiple testing correction. The table also includes information on the number of substitutions of each class observed in each gene, as well as maximum-likelihood estimates (MLEs) of the dN/dS ratios for each gene, for missense (*wmis*), nonsense (*wnon*), essential splice site mutations (*wspl*) and indels (*wind*). The global q-value integrating all mutation types are available in the *qglobal_cv* and *qallsubs_cv* columns for analyses with and without indels, respectively.

```{r}
sel_cv = dndsout$sel_cv
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