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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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AESPCA function output #54

Closed lxw391 closed 5 years ago

lxw391 commented 5 years ago

Suggest to take out the "setsize" column, (and maybe renaming "trim_size" to set size), it can be confusing for users. Typically, pathway analysis software returns the total number of genes in the pathway (after trimming) and number of deferentially expressed genes.

also why does path110 and path253 have same name, but different genes?

image

gabrielodom commented 5 years ago
  1. Set size vs. trimmed set size: should we report the number of genes removed then? We should have some way of knowing how many of the total features from the pathway were actually used.
  2. That's a Wikipathways question. Here's their documentation for
gabrielodom commented 5 years ago

For q1: remove the setsize column. This information is still retained in the -omics object. Rename trim_setsize to n_tested.

For q2: do nothing

gabrielodom commented 5 years ago

Change all mention of trim_size or trim_setsize to n_tested.