grabAccessionData {RaMS}

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)

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.

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.

Examples

library(RaMS)

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")