In tidymass/tidymass: R packages for mass spectrometry data processing and analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = TRUE,
  out.width = "100%"
)

Data preparation

Download the demo data and refer this article.

We have positive and negative mode. For each mode, we have control, case and QC groups. Control group have 110 samples, and case group have 110 samples as well.

Positive mode

massprocesser package is used to do the raw data processing. Please refer this website.

Code

The code used to do raw data processing.

library(tidymass)

process_data(
  path = "mzxml_ms1_data/POS",
  polarity = "positive",
  ppm = 10,
  peakwidth = c(10, 60),
  threads = 4,
  output_tic = FALSE,
  output_bpc = FALSE,
  output_rt_correction_plot = FALSE,
  min_fraction = 0.5,
  group_for_figure = "QC"
)

Results

All the results will be placed in the folder mzxml_ms1_data/POS/Result. More information can be found here.

You can just load the object, which is a mass_dataset class object.

load("mzxml_ms1_data/POS/Result/object")
object

We can see that there are 10,149 metabolic features in positive mode.

You can use the plot_adjusted_rt() function to get the interactive plot.

load("mzxml_ms1_data/POS/Result/intermediate_data/xdata2")
##set the group_for_figure if you want to show specific groups. And set it as "all" if you want to show all samples.
plot = 
massprocesser::plot_adjusted_rt(object = xdata2, 
                 group_for_figure = "QC", 
                 interactive = TRUE)
plot

Negative mode

The processing of negative mode is same with positive mode data.

Code

Same with positive mode, change polarity to negative.

massprocesser::process_data(
  path = "mzxml_ms1_data/NEG",
  polarity = "negative",
  ppm = 10,
  peakwidth = c(10, 60),
  threads = 4,
  output_tic = FALSE,
  output_bpc = FALSE,
  output_rt_correction_plot = FALSE,
  min_fraction = 0.5,
  group_for_figure = "QC"
)

Results

Same with positive mode.

load("mzxml_ms1_data/NEG/Result/object")
object

We can see that there are 8,804 metabolic features in negative mode.

Session information

sessionInfo()

tidymass/tidymass documentation built on April 5, 2022, 2:10 a.m.