# #——回声= FALSE,消息= FALSE,警告= FALSE --------------------- knitr: opts_chunk美元集(崩溃= TRUE,评论= " # > ")图书馆(faahKO) # #——install_IPO eval = FALSE --------------------------------------------- # # 试试http://如果不支持https:// url # (!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“上市 ") ## ---- install_IPO_suggestions eval = FALSE --------------------------------- # # 挑选峰值参数优化的例子:# BiocManager:安装(“msdata”)# #优化保留时间校正的例子和分组# #参数:# BiocManager::安装(“faahKO ") ## ---- file_choosing ------------------------------------------------------- datapath公司< -系统。file("cdf"， package = "faahKO") datafiles <- list. file("cdf"， package = "faahKO")files(datapath, recursive = TRUE, full.names = TRUE) ## ----load_IPO, message=FALSE--------------------------------------------- library(IPO) ## ----optimize_peak_picking, fig.height=7, fig.width=7, warning=FALSE----- peakpickingParameters <- getDefaultXcmsSetStartingParams('matchedFilter') #设置级别为步骤0.2和0.3(因此0.25是中心点)peakpickingParameters$step <- c(0.2, 0.3) peakpickingParameters$fwhm <- c(40，50) #只设置一个值的步骤，因此这个参数没有优化peakpickingParameters$steps <- 2次。xcmsSet <- system。time({#测量时间resultPeakpicking <- optimizeXcmsSet(files = datafiles[1:2]， params = peakpickingParameters, nSlaves = 1, subdir = NULL, plot = TRUE)}) ## ----optimize_peak_picking_result---------------------------------------- resultPeakpicking$best_settings$result optimizedXcmsSetObject <- resultPeakpicking$best_settings$xset ## ----optimize_retcor_group, fig.height=7, fig.width=7，warning = FALSE---- retcorGroupParameters <- getDefaultRetGroupStartingParams() retcorGroupParameters$profStep <- 1 retcorGroupParameters$gapExtend <- 2.7 time。RetGroup <- system。({#测量时间resultRetcorGroup < optimizeRetGroup (xset = optimizedXcmsSetObject params = retcorGroupParameters nSlaves = 1,子目录= NULL,情节= TRUE ) }) ## ---- display_settings ---------------------------------------------------- writeRScript (resultPeakpicking best_settings参数,美元resultRetcorGroup best_settings美元)# #,乘以 --------------------------------------------------------------- 时间。xcmsSet # time，优化取峰参数时间。RetGroup #时间用于优化保留时间校正和分组参数