info_pheno(): add limit(), allow use for dataset without specific trait

NEWS.md

@@ -17,6 +17,8 @@
 - Remove `info_dataset()` and `info_datasets()`; for both can be just
   use `list_datasets()`.
 
+- Include `limit` argument for `info_pheno()`.
+
 ### Bug fixes
 
 - `list_groups()` was messed up when a species was provided.

R/get_info.R

@@ -4,6 +4,7 @@
 #'
 #' @param group Name of a group of datasets
 #' @param trait Trait identifier (can be a vector)
+#' @param limit Limit on number of traits to return (if `trait` is `NULL`)
 #' @param url The URL for the GeneNetwork API
 #'
 #' @return A data frame
@@ -12,10 +13,22 @@
 #'
 #' @examples
 #' info_pheno("BXD", "10002")
+#' info_pheno("HC_M2_0606_P", limit=10)
+#' info_pheno("HC_M2_0606_P", "1436869_at")
+#' info_pheno("HXBBXH", limit=10)
 info_pheno <-
-    function(group, trait, url=gnapi_url())
+    function(group, trait=NULL, limit=NULL, url=gnapi_url())
 {
     stopifnot(length(group)==1)
+    if(is.null(trait) || trait == "") {
+        query <- paste0("traits/", group)
+        if(!is.null(limit)) {
+            query <- paste0(query, "?limit_to=", limit)
+        }
+        result <- query_gn(query, url)
+        return(list2df(result))
+    }
+
     if(length(trait) > 1) {
         result <- lapply(trait, function(trt) info_pheno(group, trait=trt, url=url))
         return(do.call("rbind_expand", result))

docs/GNapi.html

@@ -137,6 +137,16 @@ <h3>Fetch individual phenotype info</h3>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">list_datasets</span>(<span class="st">&quot;bxd&quot;</span>, <span class="st">&quot;10001&quot;</span>)</code></pre></div>
 </div>
 </div>
+<div id="fetch-trait-information" class="section level2">
+<h2>Fetch trait information</h2>
+<p>This is mostly information about QTL location (LRS score and marker).</p>
+<p>You can get all traits within a microarray dataset, possibly limiting the results to some number.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">info_pheno</span>(<span class="st">&quot;HC_M2_0606_P&quot;</span>, <span class="dt">limit=</span><span class="dv">10</span>)</code></pre></div>
+<p>Or you can use a group name, again possibly limiting the results to some number.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">info_pheno</span>(<span class="st">&quot;HXBBXH&quot;</span>, <span class="dt">limit=</span><span class="dv">10</span>)</code></pre></div>
+<p>Or you can get the information for a single trait.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">info_pheno</span>(<span class="st">&quot;HC_M2_0606_P&quot;</span>, <span class="st">&quot;1436869_at&quot;</span>)</code></pre></div>
+</div>
 <div id="fetch-sample-data-for-a-single-trait" class="section level2">
 <h2>Fetch sample data for a single trait</h2>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ph &lt;-<span class="st"> </span><span class="kw">get_pheno</span>(<span class="st">&quot;HC_M2_0606_P&quot;</span>, <span class="st">&quot;1436869_at&quot;</span>)</code></pre></div>

vignettes/GNapi.Rmd

@@ -102,6 +102,31 @@ list_datasets("bxd", "HC_M2_0606_P")
 list_datasets("bxd", "10001")
 ```
 
+## Fetch trait information
+
+This is mostly information about QTL location (LRS score and marker).
+
+You can get all traits within a microarray dataset, possibly limiting the results
+to some number.
+
+```r
+info_pheno("HC_M2_0606_P", limit=10)
+```
+
+Or you can use a group name, again possibly limiting the results to
+some number.
+
+```r
+info_pheno("HXBBXH", limit=10)
+```
+
+Or you can get the information for a single trait.
+
+```r
+info_pheno("HC_M2_0606_P", "1436869_at")
+```
+
+
 ## Fetch sample data for a single trait
 
 ```r