Merge pull request #18 from YuLab-SMU/master

merge
YuLab-SMU · Mar 15, 2023 · 2204cb9 · 2204cb9
2 parents 7e5674a + 37572b5
commit 2204cb9
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Showing 5 changed files with 12 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.25.0.001
+Version: 3.25.0.002
 Authors@R: c( person(given = "Guangchuang", family = "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),
  person(given = "Li-Gen", family = "Wang", email = "reeganwang020@gmail.com", role = "ctb"),
  person(given = "Vladislav", family = "Petyuk", email = "petyuk@gmail.com", role = "ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
-# DOSE 3.25.0.001
+# DOSE 3.25.0.002
 
++ use `inherits` to judge the class of objects (2022-11-20, Sun)
 + test whether slot in `GSON` object is NULL (e.g., `GSON@keytype`) when assigning it to enrichment result (2022-11-07, Mon)
 
 # DOSE 3.24.0

diff --git a/R/build_Anno.R b/R/build_Anno.R
@@ -6,7 +6,8 @@ build_Anno <- function(path2gene, path2name) {
  }
  Anno_clusterProfiler_Env <- get(".Anno_clusterProfiler_Env", envir= .GlobalEnv)
 
- if(class(path2gene[[2]]) == 'list') {
+ # if(class(path2gene[[2]]) == 'list') {
+ if (inherits(path2gene[[2]], "list")){
  ## to compatible with tibble
  path2gene <- cbind(rep(path2gene[[1]],
  times = vapply(path2gene[[2]], length, numeric(1))),

diff --git a/R/enricher_internal.R b/R/enricher_internal.R
@@ -129,7 +129,8 @@ enricher_internal <- function(gene,
  p.adj <- p.adjust(Over$pvalue, method=pAdjustMethod)
  qobj <- tryCatch(qvalue(p=Over$pvalue, lambda=0.05, pi0.method="bootstrap"), error=function(e) NULL)
 
- if (class(qobj) == "qvalue") {
+ # if (class(qobj) == "qvalue") {
+ if (inherits(qobj, "qvalue")) {
  qvalues <- qobj$qvalues
  } else {
  qvalues <- NA

diff --git a/R/utilities.R b/R/utilities.R
@@ -43,7 +43,8 @@ calculate_qvalue <- function(pvals) {
 
  qobj <- tryCatch(qvalue(pvals, lambda=0.05, pi0.method="bootstrap"), error=function(e) NULL)
 
- if (class(qobj) == "qvalue") {
+ # if (class(qobj) == "qvalue") {
+ if (inherits(qobj, "qvalue")) {
  qvalues <- qobj$qvalues
  } else {
  qvalues <- NA
@@ -78,8 +79,9 @@ calculate_qvalue <- function(pvals) {
  return(numeric(0))
 
  qobj <- tryCatch(qvalue(pvals, lambda=0.05, pi0.method="bootstrap"), error=function(e) NULL)
-
- if (class(qobj) == "qvalue") {
+
+ # if (class(qobj) == "qvalue") {
+ if (inherits(qobj, "qvalue")) {
  qvalues <- qobj$qvalues
  } else {
  qvalues <- NA