HTML_Pretty_Sequence: HTML_Pretty_Sequence Prepare an HTML ready

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

Description

HTML_Pretty_Sequence Prepare an HTML ready

Usage

HTML_Pretty_Sequence(
  Sequence,
  Peptides,
  Rescue = NULL,
  PerfectIsoformName = NULL,
  LineWidth = 60
)

Arguments

Sequence	String of the protein AA Sequence
Peptides	data.frame of the peptides attributed to this protein
Rescue	Not Used for now
PerfectIsoformName	Name of the Isoform as observed in the
LineWidth	Number of AA before a new line (will not include the space inside)

Value

HTML string of the sequence embedded with features included as span

Examples

library(Biostrings)
PB_FilePath <- system.file("extdata",
 "protein_bank.example.fasta",
  package = "isoformnspectRe")
ProteinBank<-readAAStringSet(
  PB_FilePath
)
Sequence <- as.vector(ProteinBank["Example"])
Peptides <- data.frame(
 Start = c(2, 2, 240),
 End = c(10, 11, 253),
 Pep = c(1.9437e-06, 0.00014334, 0.0001654),
 Proteins = c(
  "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
  "strngt.11487.1 Q8WUM4-3 strngt.11487.3 strngt.11487.2",
  "strngt.11487.2"),
 Sequence = c("ATFISVQLK", "ATFISVQLKK", "YFYFQEVFPVLAAK ")
)
Sequence <- HTML_Pretty_Sequence(Sequence,Peptides)

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