R/x_test-data.R

In MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data

#' @name x_test
#' @title Example data for \code{MetNet}: data input
#' @description \code{x_test} contains 36 selected metabolic features of
#' \code{peaklist}. It will be used as an example data set in the vignette to
#' show the functionality of the packages.
#' @docType data
#' @return \code{matrix}
#' @format \code{matrix}
#' @source
#' data("peaklist_example", package = "MetNet")
#' peaklist[, 3:dim(peaklist)[2]] <- apply(peaklist[, 3:dim(peaklist)[2]], 2,
#'     function(x) x / quantile(x, 0.75))
#' peaklist[, 3:dim(peaklist)[2]] <- log2(peaklist[, 3:dim(peaklist)[2]] + 1)
#'
#' ## function to add specific features of x (defined by m/z and retention
#' ## time) to x_test
#' addTo_x_test <- function(x_test, x, mz, rt) {
#'     mzX <- x[, "mz"]
#'     rtX <- x[, "rt"]
#'     new <- x[mzX>(mz-0.01) & mzX<(mz+0.01) & rtX>(rt-0.01) & rtX<(rt+0.01), ]
#'     x_test <- rbind(x_test, new)
#'     return(x_test)
#' }
#'
#' ## Nicotianoside IX  M+Na+ 739.3515 rt 426.1241
#' x_test <- peaklist[peaklist[, "mz"] > 739.35 & peaklist[, "mz"] < 739.36 &
#'     peaklist[, "rt"] > 426.18 & peaklist[, "rt"] < 426.2, ]
#' ## Lyciumoside I M+Na+ 653.3497
#' x_test <- addTo_x_test(x_test, peaklist, mz = 653.3497, rt = 417.46)
#' ## LyciumosideII M+Na+  815.4043
#' x_test <- addTo_x_test(x_test, peaklist, mz = 815.40, rt = 383.60)
#' ## Nicotianoside X M+Na+ 825.3503
#' x_test <- addTo_x_test(x_test, peaklist, mz = 825.35, rt = 434.38)
#' ## Nicotianoside XI M+Na+  901.39913
#' x_test <- addTo_x_test(x_test, peaklist, mz = 901.40, rt = 391.15)
#' ## NicotianosideXII M+Na+ 987.4037
#' x_test <- addTo_x_test(x_test, peaklist, mz = 987.40, rt = 398.46)
#' ## NicotianosideXIII M+Na+ 1074.4042
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1074.40, rt = 404.92)
#' ## Lyciumoside IV  M+Na+ 799.4091
#' x_test <- addTo_x_test(x_test, peaklist, mz = 799.40, rt = 411.23)
#' ## Nicotianoside I M+Na+ 885.4084
#' x_test <- addTo_x_test(x_test, peaklist, mz = 885.41, rt = 420.12)
#' ## Nicotianoside II  M+Na+ 971.4074
#' x_test <- addTo_x_test(x_test, peaklist, mz = 971.41, rt = 428.81)
#' ## Nicotianoside III  M+Na+ 945.4653
#' x_test <- addTo_x_test(x_test, peaklist, mz = 945.46, rt = 402.75)
#' ## Nicotianoside IV M+Na+ 1031.4645
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1031.46, rt = 412.40)
#' ## Nicotianoside V M+Na+ 1117.4681
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1117.46, rt = 422.19)
#' ## Attenoside (or DTG956) M+Na+ 961.4601
#' x_test <- addTo_x_test(x_test, peaklist, mz = 961.46, rt = 380.46)
#' ## DTG1042/Nicotianoside VI M+Na+ 1047.4525
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1047.46, rt = 387.28)
#' ## NicotianosideVII M+Na+ 1133.4624
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1133.46, rt = 394.70)
#' ## NicotianosideVIII M+Na+ 1219.4619
#' x_test <- addTo_x_test(x_test, peaklist, mz = 1219.46, rt = 400.99)
#' ## N-coumaroylputrescine [M+H+]+ 235.143
#' x_test <- addTo_x_test(x_test, peaklist, mz = 235.14, rt = 193.85)
#' ## N',N''-coumaroyl,caffeoylspermidine [M+H+]+ 454.23
#' x_test <- addTo_x_test(x_test, peaklist, mz = 454.23, rt = 264.43)
#' ## N-caffeoylputrescine isomer 1 [M+H+]+ 251.14
#' x_test <- addTo_x_test(x_test, peaklist, mz = 251.14, rt = 108.34)
#' ## N-caffeoylputrescine isomer 2 [M+H+]+ 251.14
#' x_test <- addTo_x_test(x_test, peaklist, mz = 251.14, rt = 143.11)
#' ## N-caffeoylspermidine [M+H+]+ 308.2
#' x_test <- addTo_x_test(x_test, peaklist, mz = 308.2, rt = 246.71)
#' ## N-feruloylputrescine [M+H+]+ 265.153
#' x_test <- addTo_x_test(x_test, peaklist, mz = 265.15, rt = 191.55)
#' ## N-feruloyl-spermidine iso1 [M+H+]+ 322.212
#' x_test <- addTo_x_test(x_test, peaklist, mz = 322.21, rt = 104.13)
#' ## N-feruloyl-spermidine iso2 [M+H+]+ 322.212
#' x_test <- addTo_x_test(x_test, peaklist, mz = 322.21, rt = 147.98)
#' ## N'-N''-dicaffeoyl -spermidine [M+H+]+ 470.23
#' x_test <- addTo_x_test(x_test, peaklist, mz = 470.23, rt = 247.15)
#' ## N'-N''-diferuloyl-spermidine/
#' ##N#,N$-Coumaroyl,sinapoyl spermidine isomer [M+H+]+ 498.260/498.261
#' x_test <- addTo_x_test(x_test, peaklist, mz = 498.26, rt = 289.05)
#' ## N'-N''-dihydrated-diferuloyl-spermidine [M+H+]+ 502.25
#' x_test <- addTo_x_test(x_test, peaklist, mz = 502.25, rt = 242.55)
#' ## unknown conjugate [M+H+]+ 411.2012
#' x_test <- addTo_x_test(x_test, peaklist, mz = 411.20, rt = 211.67)
#' ## N'-N''-caffeoyl,feruloyl spermidine iso1 [M+H+]+ 484.245
#' x_test <- addTo_x_test(x_test, peaklist, mz = 484.24, rt = 264.44)
#' ## N'-N''-caffeoyl,feruloyl spermidine iso2 [M+H+]+ 484.245
#' x_test <- addTo_x_test(x_test, peaklist, mz = 484.24, rt = 270.65)
#' ## O -Coumaroylquinic acid isomer 1 [M+H+]+  339.109
#' x_test <- addTo_x_test(x_test, peaklist, mz = 339.11, rt = 248.79)
#' ## O -Coumaroylquinic acid isomer 1 [M+H+]+  339.109
#' x_test <- addTo_x_test(x_test, peaklist, mz = 339.11, rt = 268.97)
#' ## O-caffeoylquinic acid isomer 1 [M+H+]+ 355.1014
#' x_test <- addTo_x_test(x_test, peaklist, mz = 355.10, rt = 175.75)
#' ## O-caffeoylquinic acid isomer 2 [M+H+]+ 355.1014
#' x_test <- addTo_x_test(x_test, peaklist, mz = 355.10, rt = 215.85)
#' ## O-caffeoylquinic acid isomer 3 [M+H+]+ 355.1014
#' x_test <- addTo_x_test(x_test, peaklist, mz = 355.10, rt = 241.04)
#'
#' ## change rownames (that it is accepted by formulas)
#' rownames(x_test) <- paste0("x", rownames(x_test))
#' @author Thomas Naake, \email{thomasnaake@@googlemail.com}
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