rank_PFP-methods: rank PFPscore

In aib-group/PFP: Pathway Fingerprint Framework in R

Description

rank the PFP object by the value of PFP_score.

Usage

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
)

Arguments

object,	PFP class
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

Value

a ranked PFP object.

See Also

PFP-class

Examples

data(PFP_test1)
rank_PFP(PFP_test1,
        total_rank=FALSE,
        decreasing=TRUE,
        thresh_slot="p_adj_value",
        thresh_value = 0.05)

aib-group/PFP documentation built on Dec. 27, 2020, 1:13 a.m.