getAlignedTimesCpp: Get aligned indices from MS2 extracted-ion...

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

Description

Get aligned indices from MS2 extracted-ion chromatograms(XICs) pair.

Usage

getAlignedTimesCpp(
  l1,
  l2,
  kernelLen,
  polyOrd,
  alignType,
  adaptiveRT,
  normalization,
  simType,
  B1p = 0,
  B2p = 0,
  goFactor = 0.125,
  geFactor = 40,
  cosAngleThresh = 0.3,
  OverlapAlignment = TRUE,
  dotProdThresh = 0.96,
  gapQuantile = 0.5,
  kerLen = 9L,
  hardConstrain = FALSE,
  samples4gradient = 100
)

Arguments

l1	(list) A list of numeric matrix of two columns. l1 and l2 should have same length.
l2	(list) A list of numeric matrix of two columns. l1 and l2 should have same length.
kernelLen	(integer) length of filter. Must be an odd number.
polyOrd	(integer) TRUE: remove background from peak signal using estimated noise levels.
alignType	(char) A character string. Available alignment methods are "global", "local" and "hybrid".
adaptiveRT	(numeric) Similarity matrix is not penalized within adaptive RT.
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, crossCorrelation). 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)].
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.
kerLen	(integer) In simType = crossCorrelation, length of the kernel used to sum similarity score. Must be an odd number.
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.

Value

NumericMatrix Aligned indices of l1 and l2.

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
XICs.ref <- lapply(XICs[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]], as.matrix)
XICs.eXp <- lapply(XICs[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]], as.matrix)
B1p <- 4964.752
B2p <- 5565.462
time <- getAlignedTimesCpp(XICs.ref, XICs.eXp, 11, 4, alignType = "hybrid", adaptiveRT = 77.82315,
 normalization = "mean", simType = "dotProductMasked", B1p = B1p, B2p = B2p,
 goFactor = 0.125, geFactor = 40, cosAngleThresh = 0.3, OverlapAlignment = TRUE,
 dotProdThresh = 0.96, gapQuantile = 0.5, hardConstrain = FALSE, samples4gradient = 100)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.