knitr::opts_chunk$set( collapse = TRUE, comment = "#>", warning = FALSE, message = TRUE, out.width = "100%" )
mass_data
class object can also contain MS2 data.
We need to create a mass_data
class object first, see this document. And here we use the data from this step as examples.
load("feature_table/object_pos") load("feature_table/object_neg")
The MS2 raw data should be converted to mgf format data. Please refer this document.
Here we use the demo data for tidymass
, please download it and put it in the feature_table
folder.
Then uncompress it.
mass_dataset
class objectPositive mode.
object_pos2 = mutate_ms2( object = object_pos, column = "rp", polarity = "positive", ms1.ms2.match.mz.tol = 10, ms1.ms2.match.rt.tol = 15, path = "feature_table/MS2_data/POS/" )
Negative mode.
object_neg2 = mutate_ms2( object = object_neg, column = "rp", polarity = "negative", ms1.ms2.match.mz.tol = 10, ms1.ms2.match.rt.tol = 15, path = "feature_table/MS2_data/NEG/" )
sessionInfo()
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