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How to get aligned feature list from mSet object? #4

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YasinEl opened this issue May 11, 2021 · 0 comments
Open

How to get aligned feature list from mSet object? #4

YasinEl opened this issue May 11, 2021 · 0 comments

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@YasinEl
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YasinEl commented May 11, 2021

Thank you for your package! I was wondering how it is possible to get the aligned peak list from the mSet object?

I realize that it is possible to get the unaligned peak list via:

mSet@peakpicking[["chromPeaks"]]

which is in my understanding equivalent to:

xcms::chromPeaks(XCMSnExp_object)

However, what is the mSet equivalent to:

feature_defs <- xcms::featureDefinitions(XCMSnExp_object)
feature_areas <- xcms::featureValues(XCMSnExp_object, value = "into")

df <- merge(feature_defs, feature_areas, by=0, all=TRUE)
df <- df[,!(names(df) %in% c("peakidx"))]

?

Thank you and best wishes,
Yasin

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