Protein_feature_list_fun: Protein_feature_list_fun

View source: R/Canidate_processing.R

Protein_feature_list_funR Documentation

Protein_feature_list_fun

Description

This is a function that prepare the candiate list for maldi imaging data qualitative or quantitative analysis. this function will read the fasta file and generate mz for the adducts list defined in "adducts".

Usage

Protein_feature_list_fun(
  workdir = getwd(),
  database,
  Digestion_site = "[G]",
  missedCleavages = 0:1,
  Multiple_mode = c("sequential", "parallel"),
  adducts = c("M+H", "M+NH4", "M+Na"),
  BPPARAM = bpparam(),
  Decoy_search = T,
  Decoy_mode = c("adducts", "elements", "isotope", "sequence"),
  Decoy_adducts = c("M+He", "M+Ne", "M+Ar", "M+Kr", "M+Xe", "M+Rn"),
  Substitute_AA = list(AA = c(NULL), AA_new_formula = c(NULL), Formula_with_water =
    c(NULL)),
  mzrange = c(500, 4000),
  output_candidatelist = T,
  Modifications = list(fixed = NULL, fixmod_position = NULL, variable = NULL,
    varmod_position = NULL),
  use_previous_candidates = F,
  Protein_desc_of_exclusion = NULL,
  Database_stats = F
)

Arguments

workdir

the folder that contains fasta file

database

the file name of fasta file

Digestion_site

Digestion pattern, this is the

missedCleavages

Define a number range for misscleaved peptides to be considered

adducts

the adducts list to be used for generating the PMF search candidates

BPPARAM

parallel processing parameter for BiocParallel

Value

a table of peptide candiate list

Examples

Protein_feature_list_fun(database="lipid candidates.csv",adducts=c("M+H","M+NH4","M+Na"))


MASHUOA/HiTMaP documentation built on Nov. 14, 2024, 5:23 p.m.