NEWS.md
In wilsontom/sRm: Toolkit for SRM-MS data (MS) data

sRm v0.2.4

Use the CentWave algorithm for peak detection
Remove explicit slot for transformed chromatograms
Standardise transition naming
Add peakAsymmetry method
Add method for creating peak groups
Export results using peak group IDs
Add backend as an argument in openSRM. Select either mzR (Default) or q3ML (this is hopefully a short term solution to mzML files which have been converted using newer versions of pwiz, and are currently not supported by mzR.

Breaking Changes

Multiple file input. SRM objects can be used for single mzML files or batch mode for multiple files
Basic support for peak smoothing (Savitzky-Golay implemented at present)
Support for chromatogram feature detection (pracma & xcms matchedFilter)
Improved plotting methods
Complete re-write of openSRM function and all underlying methods
All previous methods form v0.1.4 and lower; now deprecated

The main change is that extraction and decoding of chromatogram time and intensity arrays is now performed by mzR.
xml2 is still used for extraction of header data which is currently unsupported by mzR
A lot of the internal workings have been updated / replaced with more efficent approaches; mainly utilising dplyr, tibble and purrr
New method export_to_skyline exports SRM transitions in a format that can saved as .csv and uploaded to Skyline
The peaks slot in SRM-object is now a list of tibbles
index slot in SRM-object incorporates polarity (- or +)
SRM-object headeris now a tibble
Bug fix in plotAll which caused multiple outputs during layering of plots
Bug fix in plotMulti which caused switching of colours between geom_lines and labels
Bug fix in plotAll which was causing for a new index order to be created
Additional labelling options (default or custom) for plotMulti
Added vignette

Add plotMulti for easy graphical representation of complex SRM-MS chromatograms
Cleaned up filter naming throughout
Fixed CI build environment, so there is no longer a list of unnecessary Imports in DESCRIPTION
openSRMfile wasn't checking for file compression and assuming that file were converted with no compression. openSRMfile now checks for zlib compression and if found passes the gzip compression type arg to sRm::decodePeaks
Instrument, Instrument Model and Instrument Serial are all separate fields in the meta method
Internal helper function add (scanPolarity) to extract scan polarity from cvParam and insert into object@header
Parent (Q1) and product (Q3) masses are extracted from cvParams using getQMZs and are no longer string processed from filter names
filter slot added to the SRM class. This contains a raw copy of idRefs
object@header now includes scan polarity; -1 = negative, 1 = positive
totalIonCount has become totIonCount to improve readability
combineTransitions now does a "best effort" at checking for transitions which have been acquired using dynamic MRM mode
- In these circumstances; a transition set needs to consider the retention window aswell as the parent m/z
- Unique filter ID strings are created from parsed idRefs
- Where Rt lengths are unequal within unique transitions set; these are (for now) removed from the transitions class with a on-screen message stating which idRefs have been dropped

Adapt combineTransitions to catch SRM's of different lengths
Result of combineTransitions is now S3 class
Plot method for combineTransitions class ;(plotAll)
Plot method for single transition events; (plotSRM)
Bug fixed for when time and intensity arrays are encoded with different precisions
grid and gridExtra are listed as Dependencies