x_test {MetNet} | R Documentation

## Example data for `MetNet`: data input

### Description

`x_test` contains 36 selected metabolic features of `peaklist`. It will be used as an example data set in the vignette to show the functionality of the packages.

### Format

`matrix`

### Value

`matrix`

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### 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))

[Package MetNet version 1.5.3 Index]