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

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/convert_species.R

Description

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

Usage

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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 motway@cmri.org.au

See Also

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

Examples

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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.