## ----biocstyle, echo = FALSE, results = "asis"-------------------------------- BiocStyle::markdown() ## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----init, message = FALSE, echo = FALSE, results = "hide"-------------------- ## Silently loading all packages library(BiocStyle) library(peakPantheR) library(faahKO) library(pander) ## ----------------------------------------------------------------------------- library(faahKO) ## file paths input_spectraPath <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO")) input_spectraPath ## ---- eval = FALSE------------------------------------------------------------ # # targetFeatTable # input_targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), # c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", # "mz", "mzMax"))), stringsAsFactors=FALSE) # input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., # 522.194778, 522.2, 522.205222) # input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., # 496.195038, 496.2, 496.204962) # input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)], # as.numeric) ## ---- results = "asis", echo = FALSE------------------------------------------ # use pandoc for improved readability input_targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=FALSE) input_targetFeatTable[1,] <- c("ID-1", "Cpd 1", 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222) input_targetFeatTable[2,] <- c("ID-2", "Cpd 2", 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962) input_targetFeatTable[,c(3:8)] <- sapply(input_targetFeatTable[,c(3:8)], as.numeric) rownames(input_targetFeatTable) <- NULL pander::pandoc.table(input_targetFeatTable, digits = 9) ## ----------------------------------------------------------------------------- library(peakPantheR) annotation <- peakPantheR_singleFileSearch( singleSpectraDataPath = input_spectraPath, targetFeatTable = input_targetFeatTable, peakStatistic = TRUE, curveModel = 'skewedGaussian', verbose = TRUE) ## ----------------------------------------------------------------------------- annotation$TIC ## ----------------------------------------------------------------------------- ## acquisition time cannot be extracted from NetCDF files annotation$acquTime ## ---- eval = FALSE------------------------------------------------------------ # annotation$peakTable ## ---- results = "asis", echo = FALSE------------------------------------------ # use pandoc for improved readability pander::pandoc.table(annotation$peakTable, digits = 7) ## ----------------------------------------------------------------------------- annotation$curveFit ## ----------------------------------------------------------------------------- annotation$ROIsDataPoint ## ---- out.width = "700px", echo = FALSE--------------------------------------- knitr::include_graphics("../man/figures/singleFileSearch_EICsPlot.png")