RaMS (version 1.4.3)

editMSfileRTs: Edit mzML/mzXML file retention times

Description

This function uses the basic XML parsing of RaMS to modify the retention times of MS scans within the mzML/mzXML files. This method can be useful for performing RT correction using one platform and then peakpicking and correspondence on another. The basic method is simply replacing the scan's recorded retention time value with an arbitrary one of your choosing. This function is vectorized to handle multiple files, while the internal `editMzmlRTs()` and `editMzxmlRTs()` do most of the heavy lifting. Note that the seconds vs minutes must be closely monitored here - the unit should be the same as the one in the file originally.

Usage

editMSfileRTs(
  files,
  new_rt_list,
  new_filenames = NULL,
  interp_method = "linear",
  overwrite = FALSE
)

Value

Invisibly, the names of the edited files.

Arguments

files

Vector of filenames (including the relative/absolute path)

new_rt_list

Nested of new retention times. One entry in the list for each file (in the same order as the files), each containing a vector of new retention times. RT vectors can be equal to either every scan or just every MS1 scan. If only the MS1 scans are provided in a file with additional MS levels, MSn scan RTs will be interpolated according to interp_method (below)

new_filenames

Vector of filenames (including relative/absolute paths) describing where the edited files should be written out. Can be the same as files but will throw a warning and append _rtcor to each file unless `overwrite = TRUE` (below)

interp_method

Either "linear" or "constant". Describes the way that MSn retention times should be handled when only the MS1 values are provided. "linear" (the default) means that the spacing will be preserved, while "constant" will use the associated MS1 scan RT for all MSn scans, allowing an easy method of linking the MSn to the MS1.

overwrite

Boolean. Controls whether files are overwritten in place if `new_filenames` is not provided.

Examples

if (FALSE) {
# Setup (allows running on CRAN computers)
example_dir <- tempdir()
rams_dir <- system.file("extdata", package = "RaMS")
file.copy(list.files(rams_dir, pattern = "LB.*mzML", full.names = TRUE), example_dir)
mzMLs <- list.files(example_dir, pattern = "LB.*mzML", full.names = TRUE)

library(xcms)
library(RaMS)

register(SerialParam())
xcms_obj <- readMSData(mzMLs, msLevel. = 1, mode = "onDisk")
cwp <- CentWaveParam(ppm = 5, peakwidth = c(20, 80))
xcms_peakpicked <- findChromPeaks(xcms_obj, param = cwp)
xcms_rtcor <- adjustRtime(xcms_peakpicked, param = ObiwarpParam())

# Extract the adjusted RTs from the XCMS object
new_rts <- split(rtime(xcms_rtcor)/60, fromFile(xcms_rtcor))
# Apply the retention time correction to the new files
mzMLs_rtcor <- editMSfileRTs(mzMLs, new_rt_list = new_rts)

# Contrast the two chromatograms to see the peaks aligned
qplotMS1data(grabMSdata(mzMLs)$MS1[mz%between%pmppm(104.1073, 10)])
qplotMS1data(grabMSdata(mzMLs_rtcor)$MS1[mz%between%pmppm(104.1073, 10)])

# Cleanup
file.remove(mzMLs)
file.remove(mzMLs_rtcor)
}