deisotoper (version 0.0.7)

deisotoper: Construct a Deisotoper Object

Description

deisotoper returns a deisotoper object.

deisotope detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.

Usage

deisotoper(amino_acid_masses = list(A = 71.03711, R = 156.10111, N =
  114.04293, D = 115.02694, C = 103.00919, E = 129.04259, Q = 128.05858, G =
  57.02146, H = 137.05891, I = 113.08406, L = 113.08406, K = 128.09496, M =
  131.04049, F = 147.06841, P = 97.05276, S = 87.03203, T = 101.04768, W =
  186.07931, Y = 163.06333, V = 99.06841), F1 = 0.8, F2 = 0.5, F3 = 0.1,
  F4 = 0.1, F5 = 0.1, delta = 0.003, errortolerance = 0.3,
  distance = 1.00048, noise = 0, decharge = FALSE, modus = "first",
  comment = "")

Arguments

amino_acid_masses

List of amino acid masses used for scoring.

F1

F1 multiplier used for scoring.

F2

F2 multiplier used for scoring.

F3

F3 multiplier used for scoring.

F4

F4 multiplier used for scoring.

F5

F5 multiplier used for scoring.

delta

Delta value used for clustering.

errortolerance

Errortolerance used for scoring.

distance

Distance between two peaks used by clustering.

noise

Noise value for noise filtering (in percent).

decharge

De- and activates decharging.

modus

Modus of aggregation ('first' or 'highest').

comment

default is empty word.

Value

deisotoper as list of JavaRef

Details

Input: a peak peaked mass spectrum.

The algorithm: The deisotoper algorithm detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.

Output:

References

Features-Based Deisotoping Method for Tandem Mass Spectra http://dx.doi.org/10.1155/2011/210805.

See Also

deisotope

Examples

# NOT RUN {
# EXAMPLE 1
# standart configurated deisotoper
dtoper <- deisotoper()

# return the configuration of dtoper
config <- config.deisotoper(dtoper)

# example data
x <- list(mZ = c(110.07172, 111.07504, 129.10249, 130.08649, 147.11302,
   149.04506, 167.05571, 175.11923, 181.06099, 199.07158, 216.09814, 
   223.15556, 239.09503, 251.15036, 261.15579, 262.13, 280.14053,
   281.14398, 285.00974, 299.06165, 303.02039, 328.11386, 332.20789,
   344.97641, 345.14056, 350.21866, 355.06995, 360.22412, 368.17529,
   373.08078, 415.03656, 418.99521, 430.2774, 431.28107, 464.26218,
   473.3085, 476.18176, 479.20718, 481.25989, 497.21811, 521.27063,
   521.77087, 540.7804, 559.31946, 560.32391, 580.32739, 582.30688,
   592.28766, 592.35815, 593.34113, 608.25214, 610.30243, 610.36755,
   611.30554, 611.37042, 630.35724, 631.36115, 642.572, 643.054,
   643.569, 644.062, 644.557, 681.37762, 684.31494, 691.36011,
   709.37109, 709.4353, 710.44037, 712.3092, 721.33459, 754.33899,
   774.36261, 790.38892, 791.39124, 792.39221, 813.4679, 820.40479,
   823.41522, 824.40546, 825.39423, 826.39734, 840.47681, 841.43036,
   841.47949, 896.4137, 903.47253, 904.47565, 905.47632, 906.47607,
   924.46271, 951.51038, 969.52002, 970.52283, 1038.50195, 1041.53308,
   1042.53845, 1080.55493, 1081.54773),
          intensity = c(378322, 32496.6, 85689.6, 46440.3, 49645.2, 
          25102.5, 32516.2, 83497.2, 74653.1, 37228, 196053, 83826.4,
          112718, 114812, 88089.5, 61521.3, 220054, 58888.5, 280334,
          122311, 14953.2, 26959.6, 24854, 27122.9, 86216.1, 63360.3,
          358968, 47393.5, 37893.2, 16532.9, 17259, 37250.4, 33679.8,
          21243.6, 17854.9, 51232.4, 12738.8, 19515.4, 31560.1, 48772.3,
          66481.2, 23353.6, 11994, 15211, 9883.29, 14753.7, 17304.7,
          51575.9, 10917.6, 40518.3, 15107.3, 62106.4, 72496.1, 9430.4,
          10289.3, 34831.3, 41981.1, 17000, 25000, 12000, 9000, 4000,
          9579.9, 10392.3, 13507.4, 38200.9, 29990.5, 9304.39, 19849, 
          10678.6, 8452.85, 14519.3, 111717, 185030, 56020.8, 3387.69,
          9478.08, 7878.29, 3167.8, 20670.7, 2774.25, 31114.4, 3385.92,
          4656.8, 3687.15, 65332.5, 207097, 68080.9, 11934.3, 3630.86,
          9201.02, 47579.2, 19125.8, 3439.48, 15082.1, 8280.57, 4170.47,
          2603.17),
          title = "TP filtered inserted example 2 of protViz::deisotoper.",
          rtinseconds = 1581,
          charge = 2,
          scan = 1,
          id = 1,
          pepmass = 592.8093)

# deisotope the data
xd <- deisotope(dtoper, x)
summary.deisotoper(dtoper)

# plot the example data and the deisotoped data
op <- par(mfrow=c(2,2))
plot.deisotoper(x, xd)
plot.deisotoper(x, xd, xlim=c(275,285))
plot.deisotoper(x, xd, xlim=c(790,795))
plot.deisotoper(x, xd, xlim=c(901,910))
par(op)

# return the annotated spectrum of the above deisotoped data
print.deisotoper(dtoper)



# EXAMPLE 2
# standart configurated deisotoper with changed delta and decharging
dtoper2 <- deisotoper(delta = 0.005, decharge = TRUE)

# return the configuration of dtoper2
config2 <- config.deisotoper(dtoper2)

# }
# NOT RUN {
# return the GraphViz dot graphs of the above deisotoped data
xdot <- dot.deisotoper(dtoper)

# draws the isotopic cluster graphs in the browser (html)
  if(require(DiagrammeR)){
    lapply(xdot, DiagrammeR::grViz)
  }
# }
# NOT RUN {
# }