## ----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)

## ---- eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("peakPantheR")

## ---- eval = FALSE------------------------------------------------------------
#  # Install devtools
#  if(!require("devtools")) install.packages("devtools")
#  devtools::install_github("phenomecentre/peakPantheR")

## ---- eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  
#  BiocManager::install("faahKO")

## -----------------------------------------------------------------------------
library(faahKO)
## file paths
input_spectraPaths  <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
                        system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                        system.file('cdf/KO/ko18.CDF', package = "faahKO"))
input_spectraPaths

## ---- 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(1, "Cpd 1", 3310., 3344.888, 3390., 522.194778,
#                                  522.2, 522.205222)
#  input_targetFeatTable[2,] <- c(2, "Cpd 2", 3280., 3385.577, 3440., 496.195038,
#                                  496.2, 496.204962)
#  input_targetFeatTable[,c(1,3:8)] <- sapply(input_targetFeatTable[,c(1,3:8)],
#                                              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(1, "Cpd 1", 3310., 3344.888, 3390., 522.194778, 
                                522.2, 522.205222)
input_targetFeatTable[2,] <- c(2, "Cpd 2", 3280., 3385.577, 3440., 496.195038,
                                496.2, 496.204962)
input_targetFeatTable[,c(1,3:8)] <- sapply(input_targetFeatTable[,c(1,3:8)], 
                                            as.numeric)
rownames(input_targetFeatTable) <- NULL
pander::pandoc.table(input_targetFeatTable, digits = 9)