Functions that are on their way to the function afterlife. Their successors are also listed.
All functions throw a warning, with a deprecation message pointing towards its descendent (if available).
The successors of these functions are likely coming after the rework that
led to the creation of the mosdef package. See more into its
documentation for more details.
deseqresult2df(), now replaced by the more consistent
mosdef::deresult_to_df(). The only change in its functionality concerns
the parameter names
gene_plot() has now been moved to mosdef::gene_plot(), where it
generalizes with respect to the container of the DE workflow object. In a
similar fashion, get_expression_values() is replaced by
mosdef::get_expr_values(). Both functions lose the gtl parameter, which
was anyways not really exploited throughout the different calls in the
package
go_2_html() and geneinfo_2_html() have been replaced by the more
information-rich (and flexible) mosdef::go_to_html() and
mosdef::geneinfo_to_html(), respectively. No change is expected for the
end user
map2color() and styleColorBar_divergent() are now moved to the
mosdef::map_to_color() and mosdef::styleColorBar_divergent(), again with
no visible changes for the end user
The internally defined functions .link2amigo(), .link2ncbi(),
.link2genecards() and .link2gtex() are now replaced by the equivalent
functions in mosdef:
mosdef::create_link_GO(), mosdef::create_link_NCBI(),
mosdef::create_link_GeneCards() and mosdef::create_link_GO().
Notably, the mosdef package expanded on the
concept of automatically generated buttons, taking this to the extreme of
efficiency with the mosdef::buttonifier() function
# try(deseqresult2df())