Aligned XICs of peptide (ID = 4618) 14299_QFNNTDIVLLEDFQK/3 across two SWATH runs:
run1 : hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
run2 : hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML
A S4 object of 16 slots:
similarity score matrix.
Match or Mismatch matrix, residues of A and B are aligned without a gap. M(i,j) = Best score upto (i,j) given Ai is aligned to Bj.
Insert in sequence A, residue in A is aligned to gap in B. A(i,j) is the best score given that Ai is aligned to a gap in B.
Insert in sequence B, residue in B is aligned to gap in A. B(i,j) is the best score given that Bj is aligned to a gap in A.
Traceback matrices store source matrix name and direction as matrices are filled with dynamic programming.
Path matrix would represent alignment path through similarity matrix as binary-hot encoding.
Number of data-points in signal A.
Number of data-points in signal B.
Penalty for Gap opening. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
Penalty for Gap extension. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
True for Overlap alignment.
Aligned signalA indices after affine alignment.
Aligned signalB indices after affine alignment.
Cumulative score along the aligned path.
Not needed, will be removed.
Total number of gaps in the alignment path.
C++ code is exaplained at DIAlign namespace. File test_GenerateData.R has source code to generate the example data.
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