compute_kses: computing kinase-substrate enrichment score

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

computing kinase-substrate enrichment score

Description

computing kinase-substrate enrichment score

Usage

compute_kses(
  substate_vector,
  regulons_of_kinase,
  substrates_of_kinase_in_exp_count
)

Arguments

substate_vector	a vector for substrates with values indentified in current experiments.
regulons_of_kinase	a vector for substrates of a specific kinase, which with substrates identified in current experiments.
substrates_of_kinase_in_exp_count	a numeric for numbers in regulons_of_kinase vector.

Value

A numeric or NA for enrichment_score.

Author(s)

Dongdong Zhan and Mengsha Tong

References

Hernandez-Armenta C et al. Benchmarking substrate-based kinase activity inference using phosphoproteomic data[J]. Bioinformatics, 2017, 33(12): 1845-1851.

Examples

## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
## It may take a few minutes.
if(FALSE){
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/compute_kses.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "compute_kses.RData")
load("compute_kses.RData")

stochastic_enrichment_score_i <- compute_kses(
  substate_vector,
  regulons_of_kinase_i,
  substrates_of_kinase_in_exp_count
)
head(stochastic_enrichment_score_i)
}

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.