Commit 6eca4eef authored by liiskolb's avatar liiskolb
Browse files

warnings fixes

parent 11990c67
......@@ -102,9 +102,12 @@ gost <- function(query,
}
# Parameters
correction_methods <- c("g_SCS", "bonferroni", "fdr", "false_discovery_rate", "gSCS", "analytical")
if (length(correction_method)>1){
correction_method = "g_SCS"
}
## evaluate choices
correction_method <- match.arg(correction_method)
correction_method <- match.arg(correction_method, correction_methods)
if (startsWith(organism, "gp__")){
message("Detected custom GMT source request")
......@@ -128,12 +131,16 @@ gost <- function(query,
}
t <- ifelse(length(custom_bg) == 1, custom_bg <- jsonlite::unbox(custom_bg), custom_bg <- custom_bg)
}else{
if (domain_scope %in% c("custom_annotated", "custom")){
if (all(domain_scope %in% c("custom_annotated", "custom"))){
stop("Domain scope is set to custom, but no background genes detected from the input.")
}
}
domain_scopes <- c("annotated", "known", "custom", "custom_annotated")
if (length(domain_scope) > 1){
domain_scope = "annotated"
}
domain_scope <- match.arg(domain_scope)
domain_scope <- match.arg(domain_scope, domain_scopes)
body <- jsonlite::toJSON((
list(
......
......@@ -177,7 +177,7 @@ The result `data.frame` will include additional columns:
The function `gost` also allows to perform enrichment on multiple input gene lists. Multiple queries are automatically detected if the input `query` is a `list` of vectors with gene identifiers and the results are combined into identical `data.frame` as in case of single query.
```{r}
```{r warning = FALSE}
multi_gostres1 <- gost(query = list("chromX" = c("X:1000:1000000", "rs17396340",
"GO:0005005", "ENSG00000156103", "NLRP1"),
"chromY" = c("Y:1:10000000", "rs17396340",
......@@ -193,7 +193,7 @@ The column **query** in the result `data.frame` will now contain the correspondi
Another option for multiple gene lists is setting the parameter `multiquery = TRUE`. Then the results from all of the input queries are grouped according to term IDs for better comparison.
```{r}
```{r warning = FALSE}
multi_gostres2 <- gost(query = list("chromX" = c("X:1000:1000000", "rs17396340",
"GO:0005005", "ENSG00000156103", "NLRP1"),
"chromY" = c("Y:1:10000000", "rs17396340",
......
body {
max-width: 1200px;
}
h2 {
border-bottom: none;
}
#header {
background-color: red important!;
}
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