# #——feat_file、消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(SIAMCAT) fn.in。< -系统。文件(“extdata”、“feat_crc_zeller_msb_mocat_specI。tsv”,包= " SIAMCAT”) # #——read_feat,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - < read.table (fn.in壮举。壮举,9 = \ t,头= TRUE " = " stringsAsFactors = FALSE, check.names = FALSE) #看一些特性的壮举(110:114,1:2)# #——meta_file,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fn.in。元< -系统。文件(“extdata”、“num_metadata_crc_zeller_msb_mocat_specI。tsv”,包= " SIAMCAT”) # #——read_meta,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -元< - read.table (fn.in。元,9 = \ t,头= TRUE " = ", stringsAsFactors = FALSE, check.names = FALSE)头(元)# #——create_label,结果=“隐藏”,警告= FALSE, eval = FALSE - - - - - - - - - - - - - - - - - - #标签< -创建。标签(meta = meta标签=“诊断”,# = 1,控制= 0)# #——create_label_2,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - < -创建标签。标签(meta = meta标签=“诊断”,= 1,控制= 0,p。实验室=“癌症”,n。实验室=“健康”)标签信息# #——lefse_file美元,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fn.in。lefse < -系统。文件(“extdata”、“LEfSe_crc_zeller_msb_mocat_specI。tsv”,包= " SIAMCAT”) # #——read_lefse_file,结果=“隐藏”,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - meta.and。< - read.lefse (fn.in特性。lefse,行。meta = 1:6, row.samples = 7) meta <- meta.and.features$meta feat <- meta.and.features$feat ## ----lefse_label, results="hide", warning=FALSE------------------------------- label <- create.label(meta=meta, label="label", case = "cancer") ## ----read_metagenome_seq, results="hide", warning=FALSE, eval=FALSE----------- # fn.in.feat <- system.file( # "extdata", # "CHK_NAME.otus.count.csv", # package = "metagenomeSeq" # ) # feat <- read.table(fn.in.feat, sep='\t', # header=TRUE, quote='', row.names = 1, # stringsAsFactors = FALSE, check.names = FALSE # ) ## ----create_from_phyloseq, results="hide", warning=FALSE, eval=TRUE----------- data("GlobalPatterns") ## phyloseq example data label <- create.label(meta=sample_data(GlobalPatterns), label = "SampleType", case = c("Freshwater", "Freshwater (creek)", "Ocean")) # run the constructor function siamcat <- siamcat(phyloseq=GlobalPatterns, label=label) ## ----constructor, eval=FALSE-------------------------------------------------- # siamcat <- siamcat(feat=feat, label=label, meta=meta) ## ----constructor_phyloseq, eval=FALSE----------------------------------------- # siamcat <- siamcat(phyloseq=phyloseq, label=label) ## ---- eval=FALSE-------------------------------------------------------------- # eval_data(siamcat) ## ---- eval=FALSE-------------------------------------------------------------- # label(siamcat) <- new_label ## ----------------------------------------------------------------------------- phyloseq <- physeq(siamcat) tax_tab <- tax_table(phyloseq) head(tax_tab) ## ----------------------------------------------------------------------------- sessionInfo()