fasta: FASTA format reader
In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Fasta

R Documentation

FASTA format reader

Description

Implements as Rcpp module performing tryptic digests and summaries. The support is limited for protein sequences.

Usage

Fasta

Value

returns a list or vector objects.

Author(s)

Christian Panse <cp@fgcz.ethz.ch> 2006-2017

References

https://en.wikipedia.org/wiki/FASTA_format

Examples

# >sp|P12763|FETUA_BOVIN Alpha-2-HS-glycoprotein OS=Bos taurus
  fname <- system.file("extdata", name='P12763.fasta', package = "protViz")
  F <- Fasta$new(fname)
  F
  F$summary()
  F$getTrypticPeptides()
  
  plot(parentIonMass(F$getTrypticPeptides()), ssrc(F$getTrypticPeptides()),
    log='xy')
  text(parentIonMass(F$getTrypticPeptides()), ssrc(F$getTrypticPeptides()), 
    F$getTrypticPeptides(), pos=3, cex=0.5)

protViz documentation built on Feb. 16, 2023, 9:45 p.m.