fixing the risk_ccfa data object

jsilve24 · May 20, 2024 · 205ab36 · 205ab36
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Showing 6 changed files with 10 additions and 4 deletions.
diff --git a/R/RISK_CCFA.R b/R/RISK_CCFA.R
@@ -8,6 +8,6 @@
 #' @docType data
 #' @name RISK_CCFA
 #' @usage data(RISK_CCFA)
-#' @format A phyloseq object.
+#' @format An otu table, sample data table, and taxonomy table.
 #' @references Gevers D, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005. PMID: 24629344; PMCID: PMC4059512.
 NULL
diff --git a/data/RISK_CCFA.RData b/data/RISK_CCFA.RData
diff --git a/data/RISK_CCFA.rda b/data/RISK_CCFA.rda
diff --git a/man/RISK_CCFA.Rd b/man/RISK_CCFA.Rd
diff --git a/vignettes/introduction-to-fido.Rmd b/vignettes/introduction-to-fido.Rmd
@@ -115,8 +115,11 @@ library(fido)
 set.seed(899)
 
 data(RISK_CCFA)
+
+# making into a phyloseq object
+CCFA_phylo <- phyloseq(otu_table(as.matrix(RISK_CCFA_otu), taxa_are_rows = TRUE), sample_data(RISK_CCFA_sam), tax_table(as.matrix(RISK_CCFA_tax)))
 # drop low abundant taxa and samples
-dat <- RISK_CCFA %>% 
+dat <- CCFA_phylo %>% 
   subset_samples(disease_stat!="missing", 
                  immunosup!="missing") %>% 
   subset_samples(diagnosis %in% c("no", "CD")) %>% 

diff --git a/vignettes/introduction-to-fido.Rmd.orig b/vignettes/introduction-to-fido.Rmd.orig
@@ -119,8 +119,11 @@ library(fido)
 set.seed(899)
 
 data(RISK_CCFA)
+
+# making into a phyloseq object
+CCFA_phylo <- phyloseq(otu_table(as.matrix(RISK_CCFA_otu), taxa_are_rows = TRUE), sample_data(RISK_CCFA_sam), tax_table(as.matrix(RISK_CCFA_tax)))
 # drop low abundant taxa and samples
-dat <- RISK_CCFA %>% 
+dat <- CCFA_phylo %>% 
   subset_samples(disease_stat!="missing", 
                  immunosup!="missing") %>% 
   subset_samples(diagnosis %in% c("no", "CD")) %>%