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]