# #设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- eval = FALSE,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。方法=“ssgaussian”、文本=“Feature_1”,单位=“天”,ylabel =“规范化”,上校= c(“蓝色”、“耐火砖”),前缀= tempfile ()) ## ---- 消息= FALSE,警告= FALSE ---------------------------------------------- 前缀= tempfile()如果(! dir.exists(前缀)){dir.create (file.path(前缀))}(res,文件保存= sprintf(“% s / Feature_ % s_results_ % s。RData"， prefix = prefix, text = "Feature_1"， fit。方法= " ssgaussian ")) ## ---- 消息= FALSE,警告= FALSE ---------------------------------------------- 前缀= tempfile()如果(! dir.exists(前缀)){dir.create (file.path(前缀))}的特性。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)