uptakeGuess.Rd
Function to help find good initial parameters by guessing the initial uptake using a generalised inverse appraoach
uptakeGuess(res, numRep, numPeptides, numtimepoints, R, C, phi = 1)
An object of class DataFrame containing the results of the hdx-ms experiment
The number of replicates
The number of peptides
The number of timepoints
The number of residues
A matrix indicating the position of the residues in the peptides.
The maximum uptake possible. Default is 1.
A matrix of intial uptake guesses
require(RexMS)
require(dplyr)
data(BRD4_apo)
BRD4_apo <- BRD4_apo %>% filter(End < 100)
numTimepoints <- length(unique(BRD4_apo$Exposure))
Timepoints <- unique(BRD4_apo$Exposure)
numPeptides <- length(unique(BRD4_apo$Sequence))
BRD4_apo <- DataFrame(BRD4_apo)
C <- coverageHeatmap(res = BRD4_apo, plot = FALSE)
uptakeGuess(BRD4_apo,
numRep = 3,
numPeptides = numPeptides,
numtimepoints = numTimepoints,
R = 99,
C = C,
phi = 0.92)
#> [[1]]
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] 0 9.925906e-17 2.686649e-16 1.862456e-16 3.598183e-16 5.500804e-16
#> [2,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [3,] 0 8.892876e-01 9.200000e-01 9.200000e-01 8.898015e-01 9.200000e-01
#> [4,] 0 8.892876e-01 9.200000e-01 9.200000e-01 8.898015e-01 9.200000e-01
#> [5,] 0 8.892876e-01 9.200000e-01 9.200000e-01 8.898015e-01 9.200000e-01
#> [6,] 0 8.892876e-01 9.200000e-01 9.200000e-01 8.898015e-01 9.200000e-01
#> [7,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [8,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [9,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [10,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [11,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [12,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [13,] 0 8.633934e-01 7.769168e-01 6.898504e-01 6.817070e-01 7.055939e-01
#> [14,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [15,] 0 1.554270e-17 2.085759e-17 3.002036e-17 2.984396e-17 3.899956e-17
#> [16,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [17,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [18,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [19,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [20,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [21,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [22,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [23,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [24,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [25,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [26,] 0 7.798889e-01 8.151160e-01 7.712452e-01 7.961978e-01 8.193563e-01
#> [27,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [28,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [29,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [30,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [31,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [32,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [33,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [34,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [35,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [36,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [37,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [38,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [39,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [40,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [41,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [42,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [43,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [44,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [45,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [46,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [47,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [48,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [49,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [50,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [51,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [52,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [53,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [54,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [55,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [56,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [57,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [58,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [59,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [60,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [61,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [62,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [63,] 0 8.524781e-01 9.194326e-01 8.591736e-01 8.356827e-01 8.685926e-01
#> [64,] 0 0.000000e+00 1.686060e-01 1.316468e-01 5.826832e-01 8.425987e-01
#> [65,] 0 0.000000e+00 1.686060e-01 1.316468e-01 5.826832e-01 8.425987e-01
#> [66,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [67,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [68,] 0 3.258963e-04 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [69,] 0 3.258963e-04 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [70,] 0 0.000000e+00 5.530497e-02 4.031163e-02 0.000000e+00 9.872417e-02
#> [71,] 0 5.561749e-02 9.082274e-02 2.502774e-01 3.780328e-01 5.185659e-01
#> [72,] 0 5.561749e-02 9.082274e-02 2.502774e-01 3.780328e-01 5.185659e-01
#> [73,] 0 5.529160e-02 1.183914e-01 3.217333e-01 4.301564e-01 5.836470e-01
#> [74,] 0 5.529160e-02 1.183914e-01 3.217333e-01 4.301564e-01 5.836470e-01
#> [75,] 0 6.324777e-02 3.551777e-02 2.099658e-01 4.119406e-01 4.198417e-01
#> [76,] 0 6.324777e-02 3.551777e-02 2.099658e-01 4.119406e-01 4.198417e-01
#> [77,] 0 6.083872e-01 7.865208e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [78,] 0 6.083872e-01 7.865208e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [79,] 0 1.915543e-01 1.451382e-01 8.172445e-01 7.032213e-01 5.653994e-01
#> [80,] 0 1.011330e-01 1.472059e-01 3.554958e-01 5.090334e-01 7.442837e-01
#> [81,] 0 4.111815e-01 5.995924e-01 8.322129e-01 9.084720e-01 9.200000e-01
#> [82,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [83,] 0 4.111815e-01 5.995924e-01 8.322129e-01 9.084720e-01 9.200000e-01
#> [84,] 0 1.240986e-01 2.004669e-01 3.364981e-01 4.468742e-01 5.459144e-01
#> [85,] 0 1.240986e-01 2.004669e-01 3.364981e-01 4.468742e-01 5.459144e-01
#> [86,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [87,] 0 1.240986e-01 2.004669e-01 3.364981e-01 4.468742e-01 5.459144e-01
#> [88,] 0 1.240986e-01 2.004669e-01 3.364981e-01 4.468742e-01 5.459144e-01
#> [89,] 0 1.939424e-01 4.386837e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [90,] 0 1.939424e-01 4.386837e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [91,] 0 1.939424e-01 4.386837e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [92,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [93,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [94,] 0 2.796829e-01 5.079509e-01 8.911930e-01 9.014031e-01 9.123424e-01
#> [95,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [96,] 0 2.796829e-01 5.079509e-01 8.911930e-01 9.014031e-01 9.123424e-01
#> [97,] 0 2.796829e-01 5.079509e-01 8.911930e-01 9.014031e-01 9.123424e-01
#> [98,] 0 2.796829e-01 5.079509e-01 8.911930e-01 9.014031e-01 9.123424e-01
#> [99,] 0 2.796829e-01 5.079509e-01 8.911930e-01 9.014031e-01 9.123424e-01
#>
#> [[2]]
#> [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,] 0 1.394179e-16 2.486679e-16 1.775982e-16 3.546193e-16 3.920146e-16
#> [2,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [3,] 0 9.200000e-01 9.200000e-01 8.252618e-01 8.946036e-01 8.941222e-01
#> [4,] 0 9.200000e-01 9.200000e-01 8.252618e-01 8.946036e-01 8.941222e-01
#> [5,] 0 9.200000e-01 9.200000e-01 8.252618e-01 8.946036e-01 8.941222e-01
#> [6,] 0 9.200000e-01 9.200000e-01 8.252618e-01 8.946036e-01 8.941222e-01
#> [7,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [8,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [9,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [10,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [11,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [12,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [13,] 0 8.114006e-01 8.254846e-01 6.893098e-01 6.845798e-01 7.047389e-01
#> [14,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [15,] 0 1.441179e-17 2.202620e-17 2.863447e-17 3.021718e-17 4.223080e-17
#> [16,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [17,] 0 7.687989e-01 8.164207e-01 7.828245e-01 8.095710e-01 8.273476e-01
#> [18,] 0 7.687989e-01 8.164207e-01 7.828245e-01 8.095710e-01 8.273476e-01
#> [19,] 0 7.687989e-01 8.164207e-01 7.828245e-01 8.095710e-01 8.273476e-01
#> [20,] 0 7.687989e-01 8.164207e-01 7.828245e-01 8.095710e-01 8.273476e-01
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#> [34,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [35,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
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#> [39,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [40,] 0 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01 9.200000e-01
#> [41,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
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#> [43,] 0 8.207031e-01 9.180708e-01 8.506624e-01 8.292143e-01 9.045664e-01
#> [44,] 0 8.207031e-01 9.180708e-01 8.506624e-01 8.292143e-01 9.045664e-01
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#> [63,] 0 8.207031e-01 9.180708e-01 8.506624e-01 8.292143e-01 9.045664e-01
#> [64,] 0 0.000000e+00 1.123352e-01 2.684509e-01 6.368723e-01 8.395424e-01
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#> [69,] 0 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> [70,] 0 0.000000e+00 8.255280e-02 1.259698e-02 0.000000e+00 0.000000e+00
#> [71,] 0 4.738926e-02 8.208924e-02 2.815931e-01 3.888801e-01 6.055377e-01
#> [72,] 0 4.738926e-02 8.208924e-02 2.815931e-01 3.888801e-01 6.055377e-01
#> [73,] 0 7.336701e-02 1.380696e-01 3.609717e-01 4.289109e-01 6.770972e-01
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