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# devtools::load_all()
library(tidyverse)
library(data.table)
# Load the defaults ----
mzML_filenames <- list.files(system.file("extdata", package = "RaMS"),
pattern = "mzML", full.names = TRUE)
mzXML_filenames <- list.files(system.file("extdata", package = "RaMS"),
pattern = "mzXML", full.names = TRUE)
mzML_everything <- grabMSdata(mzML_filenames[1:2], grab_what = "everything", verbosity=2)
mzML_data <- grabMSdata(mzML_filenames[1:2], grab_what = c("BPC", "TIC", "MS1", "MS2", "metadata"))
mzXML_data <- grabMSdata(mzXML_filenames[1:2], grab_what = c(
"MS1", "MS2", "BPC", "TIC", "metadata"
), verbosity=2)
mzML_multi_data <- grabMSdata(mzML_filenames[2:4], grab_what = c("TIC", "MS1", "metadata"))
# Load EIC files ----
EIC_mz <- 118.0865
EIC_ppm <- 5
mzML_EIC_data <- grabMSdata(mzML_filenames[1:2], grab_what = c("EIC", "EIC_MS2"),
mz = EIC_mz, ppm = EIC_ppm, verbosity = 2)
mzXML_EIC_data <- grabMSdata(mzXML_filenames[1:2], grab_what = c("EIC", "EIC_MS2"),
mz = EIC_mz, ppm = EIC_ppm, verbosity = 2)
# Load rtrange files ----
test_rtrange <- c(5, 6)
mzML_trimmed <- grabMSdata(files = mzML_filenames[1:2],
grab_what = c("MS1", "MS2", "TIC", "BPC"),
rtrange = test_rtrange)
mzXML_trimmed <- grabMSdata(files = mzXML_filenames[1],
grab_what = c("MS1", "MS2", "TIC", "BPC"),
rtrange = test_rtrange)
test_zerorange <- c(5, 5)
mzML_zeroed <- grabMSdata(files = mzML_filenames[1:2],
grab_what = c("MS1", "MS2", "TIC", "BPC"),
rtrange = test_zerorange)
# Load prefilter files ----
no_prefilter <- -1
mzML_nofilter <- grabMSdata(files = mzML_filenames[1:2], grab_what = c("MS1"),
prefilter = no_prefilter)
major_prefilter <- 1e7
mzML_majorfilter <- grabMSdata(files = mzML_filenames[1:2], grab_what = c("MS1"),
prefilter = major_prefilter)
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