rank_PFP-methods {PFP}R Documentation

rank PFPscore

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)

[Package PFP version 1.0.0 Index]