## ---- eval=FALSE-------------------------------------------------------------- # vignette("phyloseq_analysis") ## ----load-packages, message=FALSE, warning=FALSE------------------------------ library("phyloseq") ## ---- eval=FALSE-------------------------------------------------------------- # myOTU1 <- import_RDP_cluster("path/to/my/filename.clust") ## ---- eval=FALSE-------------------------------------------------------------- # data(GlobalPatterns) # data(esophagus) # data(enterotype) # data(soilrep) ## ----------------------------------------------------------------------------- data(GlobalPatterns) GlobalPatterns ## ---- eval=FALSE-------------------------------------------------------------- # otu1 <- otu_table(raw_abundance_matrix, taxa_are_rows=FALSE) # sam1 <- sample_data(raw_sample_data.frame) # tax1 <- tax_table(raw_taxonomy_matrix) # tre1 <- read_tree(my_tree_file) ## ---- eval=FALSE-------------------------------------------------------------- # ex1b <- phyloseq(my_otu_table, my_sample_data, my_taxonomyTable, my_tree) ## ---- eval=FALSE-------------------------------------------------------------- # ex1c <- phyloseq(my_otu_table, my_sample_data) ## ----echo=FALSE--------------------------------------------------------------- topN <- 20 ## ----------------------------------------------------------------------------- data(GlobalPatterns) most_abundant_taxa <- sort(taxa_sums(GlobalPatterns), TRUE)[1:topN] ex2 <- prune_taxa(names(most_abundant_taxa), GlobalPatterns) ## ----------------------------------------------------------------------------- topFamilies <- tax_table(ex2)[, "Family"] as(topFamilies, "vector") ## ---- eval=FALSE-------------------------------------------------------------- # testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE) # f1<- filterfun_sample(topk(2)) # wh1 <- genefilter_sample(testOTU, f1, A=2) # wh2 <- c(T, T, T, F, F) # prune_taxa(wh1, testOTU) # prune_taxa(wh2, testOTU) ## ----------------------------------------------------------------------------- data(GlobalPatterns) f1<- filterfun_sample(topp(0.1)) wh1 <- genefilter_sample(GlobalPatterns, f1, A=(1/2*nsamples(GlobalPatterns))) sum(wh1) ex2 <- prune_taxa(wh1, GlobalPatterns) ## ----------------------------------------------------------------------------- print(ex2) ## ---- eval=FALSE-------------------------------------------------------------- # data(GlobalPatterns) # f1<- filterfun_sample(topf(0.9)) # wh1 <- genefilter_sample(GlobalPatterns, f1, A=(1/3*nsamples(GlobalPatterns))) # sum(wh1) # prune_taxa(wh1, GlobalPatterns) ## ----------------------------------------------------------------------------- data("enterotype") library("genefilter") flist<- filterfun(kOverA(5, 2e-05)) ent.logi <- filter_taxa(enterotype, flist) ent.trim <- filter_taxa(enterotype, flist, TRUE) identical(ent.trim, prune_taxa(ent.logi, enterotype)) identical(sum(ent.logi), ntaxa(ent.trim)) filter_taxa(enterotype, flist, TRUE) ## ----------------------------------------------------------------------------- ex3 <- subset_samples(GlobalPatterns, SampleType%in%c("Freshwater", "Ocean", "Freshwater (creek)")) ex3 ## ----------------------------------------------------------------------------- subset(sample_data(GlobalPatterns), SampleType%in%c("Freshwater", "Ocean", "Freshwater (creek)")) ## ----------------------------------------------------------------------------- ex4 <- subset_taxa(GlobalPatterns, Phylum=="Firmicutes") ex4 ## ----------------------------------------------------------------------------- randomSpecies100 <- sample(taxa_names(GlobalPatterns), 100, replace=FALSE) ex5 <- prune_taxa(randomSpecies100, GlobalPatterns) ## ---- eval=FALSE-------------------------------------------------------------- # data(GlobalPatterns) # ex2 <- transform_sample_counts(GlobalPatterns, I) ## ----------------------------------------------------------------------------- ex4<- transform_sample_counts(GlobalPatterns, threshrankfun(500)) ## ---- eval=FALSE-------------------------------------------------------------- # ex6 <- tax_glom(GlobalPatterns, taxlevel="Genus") ## ---- eval=FALSE-------------------------------------------------------------- # ex7 <- tip_glom(GlobalPatterns, speciationMinLength = 0.05) ## ---- eval=FALSE-------------------------------------------------------------- # install.packages("doParallel") # install.packages("doMC") # install.packages("doSNOW") # install.packages("doMPI")