## ----feat_file, message=FALSE------------------------------------------------- library(SIAMCAT) fn.in.feat <- system.file( "extdata", "feat_crc_zeller_msb_mocat_specI.tsv", package = "SIAMCAT" ) ## ----read_feat, message=FALSE------------------------------------------------- feat <- read.table(fn.in.feat, sep='\t', header=TRUE, quote='', stringsAsFactors = FALSE, check.names = FALSE) # look at some features feat[110:114, 1:2] ## ----meta_file, message=FALSE------------------------------------------------- fn.in.meta <- system.file( "extdata", "num_metadata_crc_zeller_msb_mocat_specI.tsv", package = "SIAMCAT" ) ## ----read_meta, warning=FALSE------------------------------------------------- meta <- read.table(fn.in.meta, sep='\t', header=TRUE, quote='', stringsAsFactors = FALSE, check.names = FALSE) head(meta) ## ----create_label, results="hide", warning=FALSE, eval=FALSE------------------ # label <- create.label(meta=meta, label="diagnosis", # case = 1, control=0) ## ----create_label_2, warning=FALSE-------------------------------------------- label <- create.label(meta=meta, label="diagnosis", case = 1, control=0, p.lab = 'cancer', n.lab = 'healthy') label$info ## ----lefse_file, message=FALSE------------------------------------------------ fn.in.lefse<- system.file( "extdata", "LEfSe_crc_zeller_msb_mocat_specI.tsv", package = "SIAMCAT" ) ## ----read_lefse_file, results="hide", warning=FALSE--------------------------- meta.and.features <- read.lefse(fn.in.lefse, rows.meta = 1:6, row.samples = 7) meta <- meta.and.features$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()