wkumler commented 2 years ago

New in this version is file minification, which shrinks the size of an MS file by removing irrelvant data points. For MS1 data, the points are decoded and filtered using data.table. For MS2 data, the entire scan is dropped if the precursor m/z isn't within the user's supplied bounds. Both inclusion lists and exclusion lists are supported, but not simultaneously.

Also new: extraction of arbitrary file metadata using grabAccessionData, which accepts a filename and a HUPO-MSI accession number and returns the data as a table. Credit to @YonghuiDong for this FR in #2.

Also, lots of bug fixes, more unit tests, increased stability as a whole.

wkumler commented 2 years ago

Once GitHub actions confirms that this passes the various checks, I'll merge it into main.

codecov-commenter commented 2 years ago

Codecov Report

Merging #3 (2449c92) into master (3f2d4c6) will decrease coverage by 2.37%. The diff coverage is 86.31%.

@@            Coverage Diff             @@
##           master       #3      +/-   ##
==========================================
- Coverage   90.01%   87.64%   -2.38%     
==========================================
  Files           3        4       +1     
  Lines         501      834     +333     
==========================================
+ Hits          451      731     +280     
- Misses         50      103      +53

Impacted Files	Coverage Δ
R/grabMSdataCode.R	`85.81% <68.57%> (-4.27%)`	:arrow_down:
R/minifyMSFunctions.R	`87.62% <87.62%> (ø)`
R/grabMzmlFunctions.R	`88.07% <100.00%> (-1.65%)`	:arrow_down:
R/grabMzxmlFunctions.R	`88.69% <100.00%> (-1.68%)`	:arrow_down:

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wkumler / RaMS

RaMS version 1.1.0 #3

Codecov Report