get_kses: computing kinase-substrate enrichment significance (pvalue)

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

computing kinase-substrate enrichment significance (pvalue)

Description

computing kinase-substrate enrichment significance (pvalue)

Usage

get_kses(substate_vector, regulons_of_kinase, trial = 1000)

Arguments

substate_vector	a vector for substrates with values identified in current experiments.
regulons_of_kinase	a vector for substrates of a specific kinase, which identified in current experiments.
trial	a numeric for the number of random samples, the default is 1000.

Value

A list for expected enrichment scores and its significance

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

## Not run: 
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/get_kses.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_kses.RData")
load("get_kses.RData")

ksea_result_i_l <- get_kses(
  ptypes_data_ratio_in_single_exp_desc,
  regulons_i_l,
  1000
)
head(ksea_result_i_l)

## End(Not run)

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