extractSignalRawData: Extract signal in a multiple defined mz rt window from a raw...

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Extract signal in a multiple defined mz rt window from a raw data file

Description

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

Usage

extractSignalRawData(rawSpec, rt, mz, msLevel = 1L, verbose = TRUE)

Arguments

rawSpec	an OnDiskMSnExp-class
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

Details

## 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

Value

a list (one entry per window) of data.frame with signal as row and retention time ('rt'), mass ('mz') and intensity ('int) as columns.

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.