extractSignalRawData {peakPantheR} | R Documentation |
Extract all signal from multiple defined mz rt window from raw data and returns a data.frame. If no rt-mz window is provided, all signal in the raw data file are returned
extractSignalRawData(rawSpec, rt, mz, msLevel = 1L, verbose = TRUE)
rawSpec |
|
rt |
(numeric(2) or two-column matrix) the lower and upper retention time range from which the data should be extracted. If a matrix is passed, each row corresponds to a different window. If not provided, the full retention time range will be extracted. |
mz |
(numeric(2) or two-column matrix) the lower and upper mass range from which the data should be extracted. If a matrix is passed, each row corresponds to a different window. If not provided, the full mass range will be extracted. |
msLevel |
(int) the MS level at which the data should be extracted (default to MS level 1) |
verbose |
(bool) If TRUE message progress and warnings |
## Examples cannot be computed as the function is not exported: ## Use a file form the faahKO package and extract data from a region of ## interest library(faahKO) rawSpec <- MSnbase::readMSData( system.file('cdf/KO/ko15.CDF',package='faahKO'), centroided=TRUE, mode='onDisk') dataPoints <- extractSignalRawData(rawSpec, rt = c(3290., 3410.), mz = c(522.194778, 522.205222), verbose=TRUE) # Reading data from 1 windows
dataPoints # [[1]] # rt mz int # 1 3290.115 522.2 1824 # 2 3291.680 522.2 1734 # 3 3293.245 522.2 1572 # 4 3294.809 522.2 1440 # 5 3299.504 522.2 1008 # 6 3301.069 522.2 871 # 7 3302.634 522.2 786 # 8 3304.199 522.2 802 # 9 3305.764 522.2 834 # 10 3307.329 522.2 839 # 11 3315.154 522.2 2187 # 12 3316.719 522.2 3534 # 13 3318.284 522.2 6338 # 14 3319.849 522.2 11718 # 15 3321.414 522.2 21744 # 16 3322.979 522.2 37872 # 17 3324.544 522.2 62424 # 18 3326.109 522.2 98408 # 19 3327.673 522.2 152896 # 20 3329.238 522.2 225984 # 21 3330.803 522.2 308672 # 22 3332.368 522.2 399360 # 23 3333.933 522.2 504000 # 24 3335.498 522.2 614656 # 25 3337.063 522.2 711872 # 26 3338.628 522.2 784704 # 27 3340.193 522.2 836608 # 28 3341.758 522.2 866304 # 29 3343.323 522.2 882304 # 30 3344.888 522.2 889280 # 31 3346.453 522.2 888256 # 32 3348.018 522.2 866816 # 33 3349.583 522.2 827392 # 34 3351.148 522.2 777728 # 35 3352.713 522.2 727040 # 36 3354.278 522.2 678464 # 37 3355.843 522.2 629120 # 38 3357.408 522.2 578048 # 39 3358.973 522.2 524288 # 40 3360.538 522.2 471040 # 41 3362.102 522.2 416320 # 42 3363.667 522.2 360064 # 43 3365.232 522.2 302400 # 44 3366.797 522.2 249152 # 45 3368.362 522.2 202560 # 46 3369.927 522.2 161024 # 47 3371.492 522.2 123520 # 48 3373.057 522.2 93160 # 49 3374.622 522.2 71856 # 50 3376.187 522.2 58392 # 51 3377.752 522.2 51072 # 52 3379.317 522.2 48376 # 53 3380.882 522.2 49168 # 54 3382.447 522.2 53120 # 55 3384.012 522.2 62488 # 56 3385.577 522.2 78680 # 57 3387.142 522.2 102840 # 58 3388.707 522.2 134656 # 59 3390.272 522.2 173440 # 60 3391.837 522.2 217088 # 61 3393.402 522.2 268864 # 62 3394.966 522.2 330496 # 63 3396.531 522.2 395776 # 64 3398.096 522.2 453376 # 65 3399.661 522.2 499072 # 66 3401.226 522.2 537024 # 67 3402.791 522.2 570304 # 68 3404.356 522.2 592512 # 69 3405.921 522.2 598912 # 70 3407.486 522.2 595008 # 71 3409.051 522.2 588416
a list (one entry per window) of data.frame with signal as row and retention time ('rt'), mass ('mz') and intensity ('int) as columns.