alignObj_DIAlignR {DIAlignR} | R Documentation

## Alignment object of a peptide.

### Description

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

### Usage

    alignObj_DIAlignR

### Format

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.

### Source

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

[Package DIAlignR version 2.2.0 Index]