RaMS (version 1.4.3)

grabAccessionData: Get arbitrary metadata from an mzML file by accession number

Description

Get arbitrary metadata from an mzML file by accession number

Usage

grabAccessionData(filename, accession_number)

Value

A data frame with the name and value of the parameter requested, as deduced from the XML tag attributes corresponding to the accession number.

Arguments

filename

The name of the file for which metadata is requested. Both absolute and relative paths are acceptable.

accession_number

The HUPO-PSI accession number for the metadata to be extracted. These accession numbers are typically of the form MS:####### and the full list can be found and searched at https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo.

Examples

library(RaMS)
data.table::setDTthreads(2)
sample_dir <- system.file("extdata", package = "RaMS")
sample_file <- list.files(sample_dir, full.names=TRUE)[3]
# Get highest observed m/z detected
topmass_df <- grabAccessionData(sample_file, "MS:1000527")
# Manually create TIC
int_df <- grabAccessionData(sample_file, "MS:1000285")
rt_df <- grabAccessionData(sample_file, "MS:1000016")
tic <- data.frame(rt=rt_df$value, int=int_df$value)
plot(tic$rt, tic$int, type = "l")