DATAFRAME_MakeALineForAIsoProt: Make a dataframe to be use in a future data table that will...

In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline

Description

Make a dataframe to be use in a future data table that will represent the protein, the peptides that match this protein, the other proteins matched with these peptides. This function can handle the Canonical form and also the isoforms

Usage

DATAFRAME_MakeALineForAIsoProt(
  LeadingRazorProtein,
  DT_Peptides,
  BS_ProteinBank,
  ProteinWidth = 60
)

Arguments

LeadingRazorProtein	Protein name as displayed in the MaxQuant seach file
DT_Peptides	Peptide data table since we are using 'Leading razor protein' and not Leading.razor.protein
BS_ProteinBank	AA StringSet protein bank.
ProteinWidth	Length of the protein displayed width. expressed in AA

Value

Dataframe with every elements needed in the displayed data frame Name name of the protein that will be displayed N_Peptides Number of peptides that match this protein PEPTIDES kable HTML ready to print table of the peptide that match this protein N_Match_Proteins Number of differents proteins that match this set of peptides Sequence HTML Ready to print sequence of the protein

Examples

library(data.table)
library(Biostrings)
library(DT)
PB_FilePath <- system.file("extdata",
 "protein_bank.example.fasta",
  package = "isoformnspectRe")
ProteinBank<-readAAStringSet(
  PB_FilePath
)
P_FilePath <- system.file("extdata",
 "peptides.example.txt",
  package = "isoformnspectRe")
Peptides<-fread(
 P_FilePath,
 integer64="double")
names(ProteinBank) <- gsub(
 " .*$",
 "",
 names(ProteinBank))
LeadingRazorProtein <-
"strngt.5372.8,start=14,stop=904,frame=2,flag=1,UNIPROT=sp|Q86U42-2|PABP2_HUMAN"
DF<-DATAFRAME_MakeALineForAIsoProt(LeadingRazorProtein,Peptides,ProteinBank)
datatable(DF,escape=FALSE)

47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.