Update for uniform first-letter capitalization

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: bugsigdbr
-Version: 1.8.1
+Version: 1.8.2
 Title: R-side access to published microbial signatures from BugSigDB
 Authors@R: c(
     person(given = "Ludwig",
@@ -37,4 +37,4 @@ License: GPL-3
 VignetteBuilder: knitr
 biocViews: DataImport, GeneSetEnrichment, Metagenomics, Microbiome
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

NEWS.md

@@ -1,5 +1,9 @@
 # bugsigdbr 
 
+## Changes in version 1.9.1
+
+* Uniform first-letter capitalization for Body site and Condition terms
+
 ## Changes in version 1.2.0
 
 * `importBugSigDB` accepts Zenodo DOIs and Github hashes to obtain

R/bugsigdb.R

@@ -37,20 +37,20 @@
 #' @return a \code{\link{data.frame}}.
 #' @references BugSigDB: \url{https://bugsigdb.org}
 #'
-#' Stable release: \url{https://doi.org/10.5281/zenodo.5606165}
+#' Stable release: \url{https://doi.org/10.5281/zenodo.10627578}
 #'
 #' Latest version (incl. not reviewed content): 
 #'      \url{https://github.com/waldronlab/BugSigDBExports}
 #'
 #' BugSigDBExports commits page:
-#'      \url{https://github.com/waldronlab/BugSigDBExports/commits/main}
+#'      \url{https://github.com/waldronlab/BugSigDBExports/commits/devel}
 #' @examples
 #'
 #'  df <- importBugSigDB()
 #'
 #' @importFrom utils read.csv
 #' @export
-importBugSigDB <- function(version = "10.5281/zenodo.6468009", cache = TRUE)
+importBugSigDB <- function(version = "10.5281/zenodo.10627578", cache = TRUE)
 {
     version <- tolower(version)
 

R/getSignatures.R

@@ -97,13 +97,13 @@ getSignatures <- function(df,
 #'
 #'  # Condition-specific meta-signatures from fecal samples, increased
 #'  # in conditions of study. Use taxonomic names instead of the default NCBI IDs:
-#'  df.feces <- df[df$`Body site` == "feces", ]
+#'  df.feces <- df[df$`Body site` == "Feces", ]
 #'  cond.meta.sigs <- getMetaSignatures(df.feces, column = "Condition", 
 #'                                      direction = "UP", tax.id.type = "taxname")
 #'
 #'  # Inspect the results
 #'  names(cond.meta.sigs)
-#'  cond.meta.sigs["bipolar disorder"]
+#'  cond.meta.sigs["Bipolar disorder"]
 #' @export
 getMetaSignatures <- function(df, 
                               column,

tests/testthat/test-getMetaSignatures.R

@@ -1,5 +1,5 @@
 bsdb <- importBugSigDB()
-df.feces <- subset(bsdb, `Body site` == "feces")
+df.feces <- subset(bsdb, `Body site` == "Feces")
 bs.msigs <- getMetaSignatures(bsdb, "Body site")
 co.msigs <- getMetaSignatures(df.feces, "Condition")
 

tests/testthat/test-getSignatures.R

@@ -2,7 +2,6 @@ bsdb <- importBugSigDB()
 
 checkSigs <- function(sigs, tax.id.type)
 {
-    sigs <- getSignatures(bsdb)
     expect_true(is.list(sigs))
     expect_true(is.character(sigs[[1]]))
     expect_true(grepl("^bsdb", names(sigs)[1]))

tests/testthat/test-ontology.R

@@ -36,21 +36,21 @@ test_that("getOntology", {
 test_that("subsetByOntology", { 
 
     bterms <- c("excreta", "digestive system", "reproductive system")
-    bpos <- list( c("feces", "meconium", "urine"), 
-                  c("stomach", "colon", "mouth"),
-                  c("vagina", "uterus", "uterine cervix"))
-    bneg <- list( c("stomach", "colon", "mouth"),
-                  c("feces", "meconium", "urine"),
-                  c("feces", "meconium", "urine"))
+    bpos <- list( c("Feces", "Meconium", "Urine"),
+                  c("Stomach", "Colon", "Mouth"),
+                  c("Vagina", "Uterus", "Uterine cervix"))
+    bneg <- list( c("Stomach", "Colon", "Mouth"),
+                  c("Feces", "Meconium", "Urine"),
+                  c("Feces", "Meconium", "Urine"))
     names(bpos) <- names(bneg) <- bterms
 
     cterms <- c("cancer", "nervous system disease", "metabolic disease")
-    cpos <- list( c("gastric cancer", "cervical cancer", "breast cancer"), 
-                  c("autism", "unipolar depression", "schizophrenia"),
-                  c("obesity", "type II diabetes mellitus", "gestational diabetes"))
-    cneg <- list( c("obesity", "anorexia nervosa", "gestational diabetes"),
-                  c("gastric cancer", "cervical cancer", "breast cancer"), 
-                  c("gastric cancer", "cervical cancer", "breast cancer"))
+    cpos <- list( c("Gastric cancer", "Cervical cancer", "Breast cancer"),
+                  c("Autism", "Unipolar depression", "Schizophrenia"),
+                  c("Obesity", "Type II diabetes mellitus", "Gestational diabetes"))
+    cneg <- list( c("Obesity", "Anorexia nervosa", "Gestational diabetes"),
+                  c("Gastric cancer", "Cervical cancer", "Breast cancer"),
+                  c("Gastric cancer", "Cervical cancer", "Breast cancer"))
     names(cpos) <- names(cneg) <- cterms
 
     for(b in bterms)