alignObj_DIAlignR: Alignment object of a peptide.
In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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

1	alignObj_DIAlignR

A S4 object of 16 slots:

s: similarity score matrix.
M: 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.
A: 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.
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: Traceback matrices store source matrix name and direction as matrices are filled with dynamic programming.
path: Path matrix would represent alignment path through similarity matrix as binary-hot encoding.
signalA_len: Number of data-points in signal A.
signalB_len: Number of data-points in signal B.
GapOpen: Penalty for Gap opening. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
GapExten: Penalty for Gap extension. For n consecutive gaps: Penalty = GapOpen + (n-1)*GapExten.
FreeEndGaps: True for Overlap alignment.
indexA_aligned: Aligned signalA indices after affine alignment.
indexB_aligned: Aligned signalB indices after affine alignment.
score: Cumulative score along the aligned path.
simScore_forw: Not needed, will be removed.
nGaps: Total number of gaps in the alignment path.