alignObj_DIAlignR | R Documentation |

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

```
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.

C++ code is exaplained at DIAlign namespace. File test_GenerateData.R has source code to generate the example data.

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