calc_PFP_score: Get the pathway fingerprint of a gene_list

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

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)

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