get_ksea_result_list: Kinase activity analysis based on known and predicted...

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

Kinase activity analysis based on known and predicted kinase-substrate relationships

Description

Kinase activity analysis based on known and predicted kinase-substrate relationships

Usage

get_ksea_result_list(
  ptypes_data_ratio_in_single_exp,
  ID,
  kinase_substrate_regulation_relationship,
  ksea_activity_i_pvalue = 0.05
)

Arguments

ptypes_data_ratio_in_single_exp	A quantification vector from a single experiment.
ID	A phosporylation ID vector like VIM_S56 (GeneSymbol_psite).
kinase_substrate_regulation_relationship	A data frame contanning kinase-substrate relationships that consists of "kinase", "substrate", "site", "sequence" and "predicted" columns.
ksea_activity_i_pvalue	A cutoff used for filtering significant activities computed from KSEA.

Value

A list containing results from ksea.

Author(s)

Dongdong Zhan and Mengsha Tong

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/get_ksea_result_list.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "get_ksea_result_list.RData")
load("get_ksea_result_list.RData")

ksea_result_list_i <- get_ksea_result_list(
 ptypes_data_ratio_in_single_exp, ID,
 kinase_substrate_regulation_relationship,
 ksea_activity_i_pvalue = 0.05
)
head(ksea_result_list_i)
}

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