get_substrate_expr_df: Get a data frame only containing kinase inferred by KSEA

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

Get a data frame only containing kinase inferred by KSEA

Description

Get a data frame only containing kinase inferred by KSEA

Usage

get_substrate_expr_df(
  ID,
  kinase_substrate_regulation_relationship,
  ksea_regulons,
  ptypes_data_ratio,
  ratio_cutoff = 3
)

Arguments

ID	A phosporylation ID vector like VIM_S56 (GeneSymbol_psite).
kinase_substrate_regulation_relationship	A data frame contanning relationship of kinase-substrate that consists of "kinase", "substrate", "site", "sequence" and "predicted" columns.
ksea_regulons	A kinase vector from ksea
ptypes_data_ratio	A data frame that the ratio of phosphorylation and profiling data
ratio_cutoff	A cutoff that depicts quantification changes at phosphorylation level relative to profiling level, the default is 3.

Value

A data frame that consists of kinase, psite, substrate, counting byond ratio_cutoff and corresponding original value.

Author(s)

Dongdong Zhan and Mengsha Tong

Examples

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

kinase_site_substrate_original_ratio_df <- get_substrate_expr_df(
  ID,
  kinase_substrate_regulation_relationship,
  ksea_regulons,
  ptypes_data_ratio,
  ratio_cutoff = 3
)
head(kinase_site_substrate_original_ratio_df)

## End(Not run)

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