rank_PFP-methods {PFP} | R Documentation |
rank the PFP object by the value of PFP_score.
rank_PFP( object, total_rank = FALSE, decreasing = TRUE, thresh_slot = "p_adj_value", thresh_value = 0.05 ) ## S4 method for signature 'PFP' rank_PFP( object, total_rank = FALSE, decreasing = TRUE, thresh_slot = "p_adj_value", thresh_value = 0.05 )
object, |
|
total_rank, |
a logical, whether to rank in total range,the default is TRUE |
decreasing, |
a logical, Sorting method, the default is TRUE |
thresh_slot, |
a character, it could be 'p_value' or 'p_adj_value', it means the threshold slot to choose for select the significant pathway. Default is 'p_adj_value'.It also could be NULL,it means that you don't want to select the significant pathway and you will select all pathways. |
thresh_value, |
a numeric, threshold value of 'p_value' or 'p_adjust_value' for pathway selection |
a ranked PFP object.
data(PFP_test1) rank_PFP(PFP_test1, total_rank=FALSE, decreasing=TRUE, thresh_slot="p_adj_value", thresh_value = 0.05)