alignObj_DIAlignR: Alignment object of a peptide.

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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.

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.