x_test: Example data for 'MetNet': data input

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

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, [e-mail]

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))

tnaake/MetNet documentation built on Nov. 4, 2024, 4:45 a.m.