create_msnset: Makes MSnSet from Quantitative Crosstab.

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Creates MSnSet object from quantitative crosstab and attached phenotype data.

Usage

create_msnset(crosstab, samples)

Arguments

samples

(table) matches sample names to reporter ions

Value

(MSnSet object) with log2-transformed relative reporter ion intensities as expression data and the samples table as phenotype data.

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, interference_score=TRUE)
masic_data <- filter_masic_data(masic_data, 0.5, 0)

# Creating cross-tab
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"))
aggregation_level <- c("accession")

crosstab <- create_crosstab(msnid, masic_data, aggregation_level, fractions, samples, references)
m <- create_msnset(crosstab, samples)
dim(m)
head(exprs(m))

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