anal_KinSub: PSP outputs of kinase-substrate interactions

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

PSP outputs of kinase-substrate interactions

Description

anal_KinSub adds the data of PSP kinase-substrate interactions to peptide or protein results.

Usage

anal_KinSub(
  db_nms = "~/proteoQ/dbs/psp/Kinase_Substrate_Dataset.txt",
  type = c("peptide", "protein"),
  match_orgs = TRUE,
  scale_log2r = TRUE,
  complete_cases = FALSE,
  impute_na = FALSE,
  df = NULL,
  filepath = NULL,
  filename = NULL,
  ...
)

Arguments

db_nms	Character string(s) to the name(s) of PSP database(s) with prepended directory path(s). Users need to download the kinase-substrate table, e.g. Kinase_Substrate_Dataset.txt directly from the PSP website and supply the corresponding file path(s) and name(s). Currently assume single database file.
type	The type of data for annotation. The default is peptide.
match_orgs	Logical; if TRUE, matches the organism between kinases and their acting substrates. The default is TRUE.
scale_log2r	Not currently used. Values before and after scaling will be both reported.
complete_cases	Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE.
impute_na	Logical; if TRUE, data with the imputation of missing values will be used. The default is FALSE.
df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
filepath	Use system default.
filename	The name of a output file.
...	filter_: Variable argument statements for the row filtration against data in a primary file linked to df. See also normPSM for the format of filter_ statements. arrange_: Variable argument statements for the row ordering against data in a primary file linked to df. See also prnHM for the format of arrange_ statements.

Details

OUtputs under folder KinSub.

Examples

# ===================================
# PhosphoSitePlus (PSP)
# ===================================

## !!!require the brief working example in `?load_expts`

library(proteoQ)

# expression data for kinases and their substrates
# (need to first download the ".txt" from PSP)
anal_KinSub("~/proteoQ/dbs/psp/Kinase_Substrate_Dataset.txt")

# `human` only ('unknown' species will be removed)
anal_KinSub(
  filter_by_sp = exprs(species == "human"),
  filter_prots_by = exprs(prot_n_pep >= 2),
  filename = human_2peps.txt,
)

# proteins
anal_KinSub(type = protein)


## Not run: 
  # peptides: CDK1 substrates
  anal_KinSub(
    filter_by_gene = exprs(species == "human", gene == "CDK1"),
    filename = hu_CDK1.txt,
  )
  
  # proteins: CDK1 substrates
  anal_KinSub(
    type = protein,
    filter_by_gene = exprs(species == "human", gene == "CDK1"),
    filename = hu_CDK1.txt,
  )

## End(Not run)

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.