{ts} add vignette tmt qc

[TomSmithCGAT]

This PR is mainly to add my first vignette!

• The short vignette deals with quality control for TMT quantification, covering the notch, missing values, signal:noise and co-isolation filtering, and summarisation to protein-level abundances.
• Adds some more tests to cover new and existing functions.
• Debugs a couple of functions where the wrong start function was called (add_PTM_positions & add_peptide_positions)
• Resolves R CMD check warnings

Something for everyone :wink:

[codecov[bot]]

Codecov Report

Merging #12 into master will increase coverage by 5.60%. The diff coverage is 13.93%.

@@            Coverage Diff             @@
##           master      #12      +/-   ##
==========================================
+ Coverage   16.96%   22.56%   +5.60%     
==========================================
  Files          17       18       +1     
  Lines         790      873      +83     
==========================================
+ Hits          134      197      +63     
- Misses        656      676      +20     

Impacted Files	Coverage Δ
R/ptm.R	0.00% <0.00%> (ø)
R/qc_plots.R	0.00% <0.00%> (ø)
R/tmt_qc_plots.R	14.40% <14.40%> (ø)
R/extract_psm_info.R	100.00% <0.00%> (ø)
R/parse_features.R	94.11% <0.00%> (+78.43%)	:arrow_up:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update f7d6ea1...3322bef. Read the comment docs.