annotating: MS annotation

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

MS annotation

Description

Annotation with chemical and biological databases

The parameters and their default values are printed for the selected database

Usage

annotating(
  x,
  database.c = c("chebi", "local.ms")[1],
  param.ls = list(query.type = c("mz", "chebi.id", "kegg.id")[1], query.col = "mz",
    ms.mode = "pos", mz.tol = 10, mz.tol.unit = "ppm", fields = c("chebi.id", "name",
    "formula", "molecular.mass", "monoisotopic.mass"), fieldsLimit = 1, max.results = 3,
    local.ms.db = data.frame(), organism = "hsa", prefix = paste0(database.c, "."), sep =
    "|"),
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiAssayExperiment'
annotating(
  x,
  database.c = c("chebi", "local.ms")[1],
  param.ls = list(query.type = c("mz", "chebi.id", "kegg.id")[1], query.col = "mz",
    ms.mode = "pos", mz.tol = 10, mz.tol.unit = "ppm", fields = c("chebi.id", "name",
    "formula", "molecular.mass", "monoisotopic.mass"), fieldsLimit = 1, max.results = 3,
    local.ms.db = data.frame(), organism = "hsa", prefix = paste0(database.c, "."), sep =
    "|"),
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'SummarizedExperiment'
annotating(
  x,
  database.c = c("chebi", "local.ms")[1],
  param.ls = list(query.type = c("mz", "chebi.id", "kegg.id")[1], query.col = "mz",
    ms.mode = "pos", mz.tol = 10, mz.tol.unit = "ppm", fields = c("chebi.id", "name",
    "formula", "molecular.mass", "monoisotopic.mass"), fieldsLimit = 1, max.results = 3,
    local.ms.db = data.frame(), organism = "hsa", prefix = paste0(database.c, "."), sep =
    "|"),
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'MultiDataSet'
annotating(
  x,
  database.c = c("chebi", "local.ms")[1],
  param.ls = list(query.type = c("mz", "chebi.id", "kegg.id")[1], query.col = "mz",
    ms.mode = "pos", mz.tol = 10, mz.tol.unit = "ppm", fields = c("chebi.id", "name",
    "formula", "molecular.mass", "monoisotopic.mass"), fieldsLimit = 1, max.results = 3,
    local.ms.db = data.frame(), organism = "hsa", prefix = paste0(database.c, "."), sep =
    "|"),
  report.c = c("none", "interactive", "myfile.txt")[2]
)

## S4 method for signature 'ExpressionSet'
annotating(
  x,
  database.c = c("chebi", "local.ms")[1],
  param.ls = list(query.type = c("mz", "chebi.id", "kegg.id")[1], query.col = "mz",
    ms.mode = "pos", mz.tol = 10, mz.tol.unit = "ppm", fields = c("chebi.id", "name",
    "formula", "molecular.mass", "monoisotopic.mass"), fieldsLimit = 1, max.results = 3,
    local.ms.db = data.frame(), organism = "hsa", prefix = paste0(database.c, "."), sep =
    "|"),
  report.c = c("none", "interactive", "myfile.txt")[2]
)

annotating_parameters(database.c = c("chebi", "local.ms", "kegg")[1])

Arguments

x	An S4 object of class SummarizedExperiment or MultiAssayExperiment
database.c	character: database to be used for annotation
param.ls	list: parameters for database query; see the example below for the name and related database of each of them
report.c	Character: File name with '.txt' extension for the printed results (call to sink()'); if 'interactive' (default), messages will be printed on the screen; if 'none', no verbose will be generated

Value

SummarizedExperiment or MultiAssayExperiment including the appended rowData data frame(s)

Examples

sacurine.se <- reading(system.file("extdata/W4M00001_Sacurine-statistics", package = "phenomis"))
# see the (default) parameters (e.g. for ChEBI query)
annotating_parameters("chebi")
# mz annotation with ChEBI
sacurine.se <- annotating(sacurine.se, database.c = "chebi", param.ls = list(query.type = "mz", query.col = "mass_to_charge", ms.mode = "neg", prefix = "chebiMZ."))
# mz annotation with local database
msdbDF <- read.table(system.file("extdata/local_ms_db.tsv", package = "phenomis"),
header = TRUE, sep = "\t", stringsAsFactors = FALSE)
sacurine.se <- annotating(sacurine.se, database.c = "local.ms",
param.ls = list(query.type = "mz", query.col = "mass_to_charge", ms.mode = "neg",
mz.tol = 5, mz.tol.unit = "ppm", local.ms.db = msdbDF, prefix = "localMS."))
rowData(sacurine.se)[!is.na(rowData(sacurine.se)[, "localMS.accession"]), ]
# annotation from ChEBI identifiers
sacurine.se <- annotating(sacurine.se, database.c = "chebi",
param.ls = list(query.type = "chebi.id", query.col = "database_identifier",
prefix = "chebiID."))
head(rowData(sacurine.se))
phenomis::annotating_parameters()
phenomis::annotating_parameters("chebi")

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.