calc_PFP_score {PFP} | R Documentation

## Get the pathway fingerprint of a gene_list

### Description

It can evaluate the performance of a gene list in the pathway networks.

### Usage

    calc_PFP_score(
      genes,
      PFPRefnet,
      lambda = 0.5,
      coeff1 = 1,
      coeff2 = 0.1,
      statistic = TRUE,
      bg_genelist = NULL,
      adjust_method = "BH"
    )

### Arguments

`genes,` | a vector of characters
`PFPRefnet,` | A PFPRefnet class
`lambda,` | a numeric, the coefficient for keeping balance between the node_score and edge_score in PFP model
`coeff1,` | a numeric, the weight coefficient for directly connected score in PFP model
`coeff2,` | a numeric, the weight coefficient for indirectly connected score in PFP model
`statistic,` | a logical,whether to do the statistical test
`bg_genelist,` | a vector of characters, background gene set for the statistical test
`adjust_method,` | statistic test method for adjust the p_value. It could be "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none".

### Details

The main part of pathway fingerprint. PFP is used to evaluate the performance of a gene_list in some pathway networks by considering the genes' topological location in a pathway. Then we can get every gene's score and the pathway score is caculated by sum all genes' score. All pathways' scores combine the pathway fingerprint.

### Value

The score of PFP

### Examples

    data(gene_list_hsa)
    data(PFPRefnet_hsa)
    PFP <- calc_PFP_score(gene_list_hsa,PFPRefnet_hsa)

[Package PFP version 1.2.0 Index]