convertSpecies: Conversion of an SRL from one species to another.

In madeleineotway/dialects: Data Independent Acquisition Library Editing to Convert The Species

Description

Converts the species in the spectral reference library to the species in the digested fasta data frame where full peptide identity occurs.

Usage

convertSpecies(digest.df = NULL, SRL.df = NULL,
  SRL.format = "peakview")

Arguments

digest.df	A data frame of the digested protein sequence from the desired species generated from digestFasta.
SRL.df	A data frame of the spectral reference library from importSRL.
SRL.format	The format of the SRL. Either "peakview" for PeakView or OneOmics SRLs or "openswath" for OpenSWATH SRLs. Defaults to "peakview".

Value

A data frame of the new spectral reference library with the peptides from the desired species.

Note

This process will remove the retention time calibration protein from a PeakView/OneOmics SRL.

Author(s)

Madeleine J Otway [e-mail]

See Also

For required functions before converting SRL, see: importFfasta, digestFasta, importSRL

Examples

data(rat_srl_example)
data(human_digest_example)
convertSpecies(human_digest_example, rat_srl_example)
convertSpecies(human_digest_example, rat_srl_example, SRL.format = "peakview")

## Workflow
fasta <- system.file("extdata",
                     "human_proteome_example.fasta",
                     package = "dialects")
human_proteome_example <- import.fasta(fasta)
human_digest_example <- digest.fasta(human_proteome_example)
srl_pv <- system.file("extdata",
                      "rat_srl_example.txt",
                      package = "dialects")
rat_srl_example <- import.srl(srl_pv, SRL.format = "peakview")
convertSpecies(human_digest_example, rat_srl_example)

madeleineotway/dialects documentation built on May 29, 2019, 3:43 a.m.