In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

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

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In this version, we just added a new function output_eic(). This can be used to generate peaks in some samples after you run process_data(). For example, you analyzed data, and found some features are very important, so you want to check the peak shapes of them in QC samples, so you can use output_eic() function.

Set work directory

First, you need to set the work directory to the folder which you used to run the process_data() function. For example, in our example for process_Data, we set the work directory in example/POS, so here, we also set work directory in this folder.

Run output_eic()

Then we can run output_eic() function.

library(metflow2)

output_eic(path = ".", 
           query_sample_name = c("QC_1"), 
           query_peak_name = c("M70T54_POS", "M70T579_POS"),
           polarity = "positive", 
           threads = 4)

Then the peak shape of plots will be outputted in example/POS/Result.

jaspershen/metflow2 documentation built on Aug. 15, 2021, 4:38 p.m.