get_summary_from_ksea: Get a data frame only containing inforamtion of kinase...

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

Get a data frame only containing inforamtion of kinase inferred by KSEA

Description

Get a data frame only containing inforamtion of kinase inferred by KSEA

Usage

get_summary_from_ksea(
  ptypes_data,
  species = "human",
  log2_label = TRUE,
  ratio_cutoff = 3
)

Arguments

ptypes_data	A data frame of phosphorylation data after normalization.
species	A string representing the species of imported data, the options are human, mouse and rat.
log2_label	A boolean value representing whether data is logarithmetics, the default is FALSE.
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

## 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_summary_from_ksea.RData"
    load_data <- load_data_with_ftp(ftp_url, 'RData')
    writeBin(load_data, "get_summary_from_ksea.RData")
    load("get_summary_from_ksea.RData")

    summary_df_list_from_ksea_cluster <- get_summary_from_ksea(
      cluster_df, species = 'human',
      log2_label = FALSE, ratio_cutoff = 3
    )
    head(summary_df_list_from_ksea_cluster)
}

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