HTML_PrettyBlastSequence: HTML_PrettyBlastSequence prepare and HTML ready string with...

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

Description

HTML_PrettyBlastSequence prepare and HTML ready string with some more informations

Usage

HTML_PrettyBlastSequence(Sequence, Peptides, Rescue, 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
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.