Splits PTMsigDB pathways by direction (up/down) and runs fgsea twice per contrast (ascending and descending rank order).
Usage
run_ptmsea_up_down(
ranks_list,
pathways,
min_size = 3,
max_size = 500,
n_perm = 1000,
pvalueCutoff = 0.1
)Arguments
- ranks_list
Named list of named numeric vectors from ptmsea_data_prep().
- pathways
Named list of pathway definitions (e.g., from fgsea::gmtPathways()).
- min_size
Integer. Minimum pathway size. Default 3.
- max_size
Integer. Maximum pathway size. Default 500.
- n_perm
Integer. Number of permutations. Default 1000.
- pvalueCutoff
Numeric. Adjusted p-value cutoff. Default 0.1.