alignChromatogramsCpp: Aligns MS2 extracted-ion chromatograms(XICs) pair.

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

Aligns MS2 extracted-ion chromatograms(XICs) pair.

Usage

alignChromatogramsCpp(
  l1,
  l2,
  alignType,
  tA,
  tB,
  normalization,
  simType,
  B1p = 0,
  B2p = 0,
  noBeef = 0L,
  goFactor = 0.125,
  geFactor = 40,
  cosAngleThresh = 0.3,
  OverlapAlignment = TRUE,
  dotProdThresh = 0.96,
  gapQuantile = 0.5,
  hardConstrain = FALSE,
  samples4gradient = 100,
  objType = "heavy"
)

Arguments

l1	(list) A list of numeric vectors. l1 and l2 should have same length.
l2	(list) A list of numeric vectors. l1 and l2 should have same length.
alignType	(char) A character string. Available alignment methods are "global", "local" and "hybrid".
tA	(numeric) A numeric vector. This vector has equally spaced timepoints of XIC A.
tB	(numeric) A numeric vector. This vector has equally spaced timepoints of XIC B.
normalization	(char) A character string. Normalization must be selected from (L2, mean or none).
simType	(char) A character string. Similarity type must be selected from (dotProductMasked, dotProduct, cosineAngle, cosine2Angle, euclideanDist, covariance, correlation). Mask = s > quantile(s, dotProdThresh) AllowDotProd= [Mask × cosine2Angle + (1 - Mask)] > cosAngleThresh s_new= s × AllowDotProd
B1p	(numeric) Timepoint mapped by global fit for tA[1].
B2p	(numeric) Timepoint mapped by global fit for tA[length(tA)].
noBeef	(integer) It defines the distance from the global fit, upto which no penalization is performed. The window length = 2*noBeef.
goFactor	(numeric) Penalty for introducing first gap in alignment. This value is multiplied by base gap-penalty.
geFactor	(numeric) Penalty for introducing subsequent gaps in alignment. This value is multiplied by base gap-penalty.
cosAngleThresh	(numeric) In simType = dotProductMasked mode, angular similarity should be higher than cosAngleThresh otherwise similarity is forced to zero.
OverlapAlignment	(logical) An input for alignment with free end-gaps. False: Global alignment, True: overlap alignment.
dotProdThresh	(numeric) In simType = dotProductMasked mode, values in similarity matrix higher than dotProdThresh quantile are checked for angular similarity.
gapQuantile	(numeric) Must be between 0 and 1. This is used to calculate base gap-penalty from similarity distribution.
hardConstrain	(logical) if false; indices farther from noBeef distance are filled with distance from linear fit line.
samples4gradient	(numeric) This parameter modulates penalization of masked indices.
objType	(char) A character string. Must be either light, medium or heavy.

Value

affineAlignObj (S4class) A S4class object from C++ AffineAlignObj struct.

Author(s)

Shubham Gupta, [e-mail] ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + MIT Date: 2019-03-08

Examples

data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR
data(oswFiles_DIAlignR, package="DIAlignR")
oswFiles <- oswFiles_DIAlignR
XICs.ref <- XICs[["run1"]][["14299_QFNNTDIVLLEDFQK/3"]]
XICs.eXp <- XICs[["run2"]][["14299_QFNNTDIVLLEDFQK/3"]]
tVec.ref <- XICs.ref[[1]][["time"]] # Extracting time component
tVec.eXp <- XICs.eXp[[1]][["time"]] # Extracting time component
B1p <- 4964.752
B2p <- 5565.462
noBeef <- 77.82315/3.414
l1 <- lapply(XICs.ref, `[[`, 2)
l2 <- lapply(XICs.eXp, `[[`, 2)
AlignObj <- alignChromatogramsCpp(l1, l2, alignType = "hybrid", tA = tVec.ref, tB = tVec.eXp,
 normalization = "mean", simType = "dotProductMasked", B1p = B1p, B2p = B2p, noBeef = noBeef,
 goFactor = 0.125, geFactor = 40, cosAngleThresh = 0.3, OverlapAlignment = TRUE,
 dotProdThresh = 0.96, gapQuantile = 0.5, hardConstrain = FALSE, samples4gradient = 100,
 objType = "light")

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.