DATAFRAME_MakeALineForABlastProt: 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 is dedicated to Blast forms, since it will compare two sequences and higlight differences.

Usage

DATAFRAME_MakeALineForABlastProt(
  LeadingRazorProtein,
  DT_Peptides,
  Rescue,
  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
Rescue	Dataframe of a blast results
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 BlastHit name of the protein from the known protein bank that match the displayed protein N_Peptides Number of peptides that match this protein Match_Proteins Proteins match by this set of peptides 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 SAAV Boolean that indicate if this protein have an SAAV SAAVxPep Boolean that indicate if this protein have peptide that display an SAAV Insertion Boolean that indicate if this protein have an Insertion InsertionxPep Boolean that indicate if this protein have a peptide that displayed a Insertion Deletion Boolean that indicate if this protein have an deletion DeletionxPep Boolean that indicate if this protein have a peptide that displayed a Deletion OutOfBlast Boolean that indicate if this protein have a peptide that display a section out of the blast, i.e. a part that is specific

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")
R_FilePath <- system.file("extdata",
 "blast_rescue.example.txt",
  package = "isoformnspectRe")
Rescue<-read.table(
 R_FilePath,
 header=TRUE)

names(ProteinBank) <- gsub(
 " .*$",
 "",
 names(ProteinBank))
LeadingRazorProtein <-
"strngt.16858.3,start=259,stop=4446,frame=1,flag=LonguestORF,Origin=3',Blast=sp|Q15596|NCOA2_HUMAN"
DF <- DATAFRAME_MakeALineForABlastProt(
LeadingRazorProtein,
Peptides,
Rescue,
ProteinBank)
datatable(DF,escape=FALSE)
ToRepresent<-DF[,c(
 "Name",
 "BlastHit",
 "N_Peptides",
 "Match_Proteins",
 "N_Match_Proteins",
 "Sequence")]
datatable(ToRepresent,escape=FALSE)

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