RenderAnIsoform: Title

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

Description

Title

Usage

RenderAnIsoform(
  IsoformProt,
  ProteinBankFastaFilePath,
  PepFilePath,
  SampleDescriptionFilePath,
  IntensityPrefix,
  SampleGroupName,
  SampleName,
  OutputDir = "./"
)

Arguments

IsoformProt	Name of the protein as displayed in the peptide file, most likely the first word(no space) of the fasta protein bank name.
ProteinBankFastaFilePath	Path to the fasta file that have been used for this analysis
PepFilePath	Path to the peptide file
SampleDescriptionFilePath	Path to the sample description file
IntensityPrefix	Prefix of the intensity, keep the space in case of
SampleGroupName	Name of the Sample group column in the Sample description file
SampleName	Name of the Sample column in the Sample description file
OutputDir	Name of the output directory, the isoform html file will be created in the isoform skelton subdirectory

Examples

library(rmarkdown)
library("flexdashboard")
library("sessioninfo")
library("sparkline")
ProteinBankFastaFilePath <- system.file("extdata",
 "protein_bank.example.fasta",
  package = "isoformnspectRe")
PepFilePath <- system.file("extdata",
 "peptides.example.txt",
  package = "isoformnspectRe")
IntensityPrefix <- "Intensity "
Pep<-read.table(PepFilePath, header=TRUE,sep="\t",quote="\"")
ProteinOfInterest <- unique(Pep$Leading.razor.protein)
ProteinOfInterest <- ProteinOfInterest[grep("UNIPROT=",ProteinOfInterest)]
ProteinOfInterest <- ProteinOfInterest[grep("-",ProteinOfInterest)][1]
SampleDescriptionFilePath <- system.file("extdata",
 "SampleDescription.txt",
  package = "isoformnspectRe")
SampleGroupName <- "LooseSampleGroup"
SampleName <- "SampleName"
RenderAnIsoform(IsoformProt=ProteinOfInterest,
 ProteinBankFastaFilePath=ProteinBankFastaFilePath,
 PepFilePath=PepFilePath,
 SampleDescriptionFilePath=SampleDescriptionFilePath,
 IntensityPrefix=IntensityPrefix,
 SampleGroupName=SampleGroupName,
 SampleName=SampleName,
 OutputDir=tempdir())

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