deprecated: Deprecated functions in GeneTonic

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Deprecated functions in GeneTonic

Description

Functions that are on their way to the function afterlife. Their successors are also listed.

Arguments

...	Ignored arguments.

Details

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.

Value

All functions throw a warning, with a deprecation message pointing towards its descendent (if available).

Transitioning to the mosdef framework

• 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• go_2_html() and geneinfo_2_html() have been replaced by the more information-rich (and flexible) mosdef::go_to_html() and mosdef::geneinfo_to_html(), respectively.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

Author(s)

Federico Marini

Examples

# try(deseqresult2df())

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.