# #设置,包括= FALSE ---------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- 结果= '隐藏',消息= FALSE,警告= FALSE -------------------------- 如果(!requireNamespace("BiocManager"， quiet = TRUE))安装。包(“BiocManager回购= " http://cran.us.r-project.org ") BiocManager::安装(“OmicsLonDA ") ## ---- 结果= '隐藏',消息= FALSE,警告= FALSE ------------------------- 库(OmicsLonDA)库(SummarizedExperiment) # # 10模拟负载特性和元数据数据(“omicslonda_data_example ") ## ------------------------------------------------------------------------ omicslonda_data_example ome_matrix美元[1:5,1:5 ] ## ------------------------------------------------------------------------ 头(omicslonda_data_example $元数据)# # = FALSE,消息,警告= FALSE ----------------------------------------- se_ome_matrix = as.matrix (omicslonda_data_example ome_matrix美元)se_metadata = DataFrame (omicslonda_data_example元数据)美元omicslonda_se_object = SummarizedExperiment(化验= (se_ome_matrix)列表,colData = = FALSE se_metadata) # #——消息,警告= FALSE ----------------------------------------- omicslonda_se_object_adjusted = adjustBaseline (se_object = omicslonda_se_object ) ## ------------------------------------------------------------------------ 分析(omicslonda_se_object_adjusted) [1:5, 1:5) # # = FALSE,消息,警告= FALSE ----------------------------------------- omicslonda_test_object = omicslonda_se_object_adjusted [1] visualizeFeature (se_object = omicslonda_test_object,文本=“Feature_1”、单位=“天”,ylabel =“规范化”,上校= c(“蓝色”、“耐火砖”),前缀= tempfile ()) ## ------------------------------------------------------------------------ 点= seq(500,长度。= 500) # #——结果=“隐藏”,消息= FALSE,警告= FALSE ------------------------- res = omicslonda (se_object = omicslonda_test_object n.perm = 10,健康。method = " ss高斯"，points = points, text = "Feature_1"， parall = FALSE, pvalue。阈值= 0.05，调整。method = "BH"，时间。单位= "天",ylabel =“正常化”,上校= c(“蓝色”、“耐火砖”),前缀= tempfile ()) ## ---- 消息= FALSE,警告= FALSE ----------------------------------------- visualizeFeatureSpline (se_object = omicslonda_test_object omicslonda_object = res,健康。method = "ssgaussian"， text = "Feature_1"， unit = "days"， ylabel = "Normalized Count"， col = c("blue"， "firebrick")， prefix = "OmicsLonDA_example") ## ----results='hide'， message=FALSE,warning=FALSE------------------------- visualizeteststatthistogram (omicslonda_object = res, text = "Feature_1"， fit. info = " info . info ")方法= " ssgaussian”前缀= tempfile ()) ## ---- 消息= FALSE,警告= FALSE ----------------------------------------- visualizeArea (omicslonda_object = res,健康。method = "ssgaussian"， text = "Feature_1"， unit = "days"， ylabel = "Normalized Count"， col = c("blue"， "firebrick")， prefix = tempfile()) ## ----message=FALSE,warning=FALSE----------------------------------------- prefix = tempfile() if (!dir.exists(prefix)){dir.create(file.path(prefix))} ## Save OmicsLonDA results in RData file Save (res, file = sprintf("%s/Feature_%s_results_%s. ")RData"， prefix = prefix, text = "Feature_1"， fit。method = " ss高斯"))##在csv文件feature中保存时间间隔统计的摘要。summary = as.data.frame(do.call(cbind, res$details)， stringsAsFactors = FALSE)summary, file = sprintf("%s/Feature_%s_Summary_%s.csv"， prefix = prefix, text = "Feature_1"， fit。方法= " ss高斯")，row.names = FALSE)