deprecated: Deprecated functions in ideal

In federicomarini/ideal: Interactive Differential Expression AnaLysis

Deprecated functions in ideal

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

• goseqTable() is now being replaced by the more flexible mosdef::run_goseq() function (which is even faster)

• ggplotCounts() is now being replaced by the more flexible, better designed, and actually even more good looking mosdef::gene_plot() function, with better default behavior and all.

• deseqresult2tbl() and deseqresult2DEgenes() are now replaced by the more flexible mosdef::deresult_to_df()

• The internally defined functions createLinkENS(), createLinkGeneSymbol(), and createLinkGO() are now replaced by the equivalent functions in mosdef: mosdef::create_link_ENSEMBL(), mosdef::create_link_NCBI() 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(goseqtable())

federicomarini/ideal documentation built on Sept. 29, 2024, 8:49 p.m.