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Merge calculateFragments and calculateFragments2 #19

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merged 30 commits into from
Jan 22, 2025
Merged

Merge calculateFragments and calculateFragments2 #19

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11d943c
Create fragments-calculate2.R
guideflandre Dec 19, 2024
32dd91b
Create test_fragments2.R
guideflandre Dec 19, 2024
ab01551
Update fragments-calculate2.R
guideflandre Dec 19, 2024
d1951bb
Update fragments-calculate2.R
guideflandre Dec 19, 2024
d505a3d
Update fragments-calculate2.R
guideflandre Dec 19, 2024
b75af03
Update documentation
guideflandre Dec 19, 2024
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Update documentation
guideflandre Dec 20, 2024
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Delete PSMatch.Rproj
guideflandre Dec 24, 2024
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Update NEWS.md
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7c8f6c9
Update DESCRIPTION
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9d1ea08
Update fragments-calculate2.R
guideflandre Dec 24, 2024
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Update test_fragments2.R
guideflandre Dec 24, 2024
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Update R/fragments-calculate2.R
guideflandre Jan 2, 2025
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Update fragments-calculate2.R
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Update fragments-calculate2.R
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Update DESCRIPTION
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git ignore Rproj file
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update .cumsumFragmentMasses
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update: testthat .cumsumFragmentMasses
guideflandre Jan 7, 2025
5c0344e
update variable_modifications default to empty numeric
guideflandre Jan 7, 2025
a39cbee
Update fragments-calculate2.R
guideflandre Jan 10, 2025
0525f86
Add warning for modifications parameter
guideflandre Jan 17, 2025
f4a5d0f
Remove redundancy in strplit(sequence)
guideflandre Jan 20, 2025
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Update documentation
guideflandre Jan 20, 2025
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update documentation
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update documentaton
guideflandre Jan 20, 2025
7107718
Merge calculateFragments and calculateFragments2 into one true calcul…
guideflandre Jan 20, 2025
4f5795a
Remove redundancies and update calculateFragments based on PR
guideflandre Jan 21, 2025
5f46152
Updated failed unit test
guideflandre Jan 21, 2025
56aec17
Update comments in addFragments
guideflandre Jan 21, 2025
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1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -4,7 +4,6 @@ export("reduced<-")
export(ConnectedComponents)
export(PSM)
export(addFragments)
export(calculateFragments2)
export(ccMatrix)
export(connectedComponents)
export(defaultNeutralLoss)
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6 changes: 6 additions & 0 deletions R/fragments-add.R
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Expand Up @@ -80,6 +80,12 @@ addFragments <- function(x,
x_data <- Spectra::peaksData(x)[[1L]]
y_data <- calculateFragments(y, verbose = FALSE, ...)
y_data <- y_data[order(y_data$mz), ]

## stop if variable modifications used
## Temporary check to allow plotSpectra to work fine
## Will need to be removed once plotSpectra accepts variable modifications
## See issue: https://github.com/rformassspectrometry/Spectra/issues/346
stopifnot(length(unique(y_data[["peptide"]])) == 1)

## Find common peaks and prepare annotations
idx <- which(MsCoreUtils::common(x_data[, "mz"], y_data[, "mz"],
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