motrpac_bic_output: Format Tables for BIC

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Assembles data in format compliant with BIC requirements.

• make_rii_peptide_gl(): returns 'RII_peptide.txt' table formatted for BIC (global)

• make_results_ratio_gl(): returns 'results_ratio.txt' table (global)

• make_rii_peptide_ph(): returns 'RII_peptide.txt' table (phospho)

• make_results_ratio_ph(): returns 'results_ratio.txt' table (phospho)

• assess_redundant_proteins(): appends proteins matched to multiple peptides

• assess_noninferable_proteins(): appends proteins with identical peptide sets

Usage

make_rii_peptide_gl(
  msnid,
  masic_data,
  fractions,
  samples,
  references,
  org_name = "Rattus norvegicus"
)

make_results_ratio_gl(
  msnid,
  masic_data,
  fractions,
  samples,
  references,
  org_name = "Rattus norvegicus"
)

make_rii_peptide_ph(
  msnid,
  masic_data,
  fractions,
  samples,
  references,
  org_name = "Rattus norvegicus",
  sep = "_"
)

make_results_ratio_ph(
  msnid,
  masic_data,
  fractions,
  samples,
  references,
  org_name = "Rattus norvegicus",
  sep = "_"
)

assess_redundant_protein_matches(msnid, collapse = "|")

assess_noninferable_proteins(msnid, collapse = "|")

Arguments

msnid	(MSnID-object) final filtered version of MSnID object
masic_data	(data.frame) final filtered version of MASIC table
fractions	(data.frame) Study design table linking Dataset with PlexID
samples	(data.frame) Study design table linking sample names with TMT channels and PlexID
references	(data.frame) Study design table describing reference value calculation
org_name	(character) Organism name. Default is 'Rattus norvegicus'
sep	(character) Single character used to concatenate protein, SiteID, and peptide

Examples

# Prepare MS/MS IDs
path_to_MSGF_results <- system.file("extdata/global/msgf_output", package = "PlexedPiperTestData")
msnid <- read_msgf_data(path_to_MSGF_results)
msnid <- MSnID::correct_peak_selection(msnid)
show(msnid)
msnid <- filter_msgf_data_peptide_level(msnid, 0.01)
show(msnid)
path_to_FASTA <- system.file("extdata/Rattus_norvegicus_NCBI_RefSeq_2018-04-10.fasta.gz", package = "PlexedPiperTestData")
msnid <- compute_num_peptides_per_1000aa(msnid, path_to_FASTA)
msnid <- filter_msgf_data_protein_level(msnid, 0.01)
show(msnid)

# Prepare table with reporter ion intensities
path_to_MASIC_results <- system.file("extdata/global/masic_output", package = "PlexedPiperTestData")
masic_data <- read_masic_data(path_to_MASIC_results, extra_metrics=TRUE)
masic_data <- filter_masic_data(masic_data, 0.5, 0)

library(readr)
fractions <- read_tsv(system.file("extdata/study_design/fractions.txt", package = "PlexedPiperTestData"))
samples <- read_tsv(system.file("extdata/study_design/samples.txt", package = "PlexedPiperTestData"))
references <- read_tsv(system.file("extdata/study_design/references.txt", package = "PlexedPiperTestData"))

results_ratio <- make_results_ratio_gl(msnid, masic_data, fractions, samples, references, org_name = "Rattus norvegicus")
rii_peptide <- make_rii_peptide_gl(msnid, masic_data, fractions, samples, references, org_name = "Rattus norvegicus")

vladpetyuk/PlexedPiper documentation built on June 24, 2021, 8:59 a.m.