Merge pull request #35 from jasenfinch/devel

v0.5.7
jasenfinch · Sep 27, 2021 · 61fdebf · 61fdebf
2 parents 6bb010c + d358221
commit 61fdebf
Show file tree

Hide file tree

Showing 28 changed files with 293 additions and 34 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metaboMisc
 Title: Miscellaneous Functions for Metabolomics Analyses
-Version: 0.5.6
+Version: 0.5.7
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Miscellaneous helper functions for metabolomics analyses that do not yet have a permanent home.
 URL: https://jasenfinch.github.io/metaboMisc
@@ -42,5 +42,4 @@ Remotes: aberHRML/binneR,
     jasenfinch/metabolyseR,
     jasenfinch/profilePro,
     jasenfinch/MFassign,
-    aberHRML/metaboData,
     jasenfinch/grover
diff --git a/NAMESPACE b/NAMESPACE
@@ -22,6 +22,7 @@ export(exportSummarisedAssignments)
 export(featureSummary)
 export(preTreatModes)
 export(reduce)
+export(sanitiseTable)
 export(suitableParallelPlan)
 exportMethods(plotRSD)
 importFrom(MFassign,assignedData)
@@ -42,6 +43,7 @@ importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_all)
 importFrom(dplyr,mutate)
+importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
 importFrom(dplyr,n_distinct)
 importFrom(dplyr,rename)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# metaboMisc 0.5.7
+
+* Removed `aberHRML/metaboData` from the Remotes field in the DESCRIPTION to ensure that the CRAN version  of metaboData is installed.
+
+* Added `sanitiseTable()` that can be used to restrict the number of  rows in a table and round numeric columns to a given number of significant figures. 
+
 # metaboMisc 0.5.6
 
 * Fixed missing argument error in `detectPretreatmentParameters()` when miss injections are detected.

diff --git a/R/sanitise.R b/R/sanitise.R
@@ -0,0 +1,21 @@
+#' Sanitise a data table
+#' @description  Sanitise a data table by restricting the number of rows and rounding numeric columns.
+#' @param x A tibble or data.frame containing the data to be sanitised
+#' @param maxRows Maximum number of rows with which to restrict the table
+#' @param sigFig Significant figures with which to round numeric columns
+#' @examples
+#' sanitiseTable(iris,maxRows = 10,sigFig = 1)
+#' @importFrom dplyr mutate_if
+#' @export
+
+
+sanitiseTable <- function(x,maxRows = 5000,sigFig = 3){
+    x <- mutate_if(x,is.numeric,signif,digits = sigFig)
+
+    if (nrow(x) > maxRows){
+        message(str_c('Number of rows in table restricted to ',maxRows,'.'))
+        x <- x[seq_len(maxRows),]
+    }
+
+    return(x)
+}
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.11.4
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2021-09-21T08:03Z
+last_built: 2021-09-27T10:19Z
 urls:
   reference: https://jasenfinch.github.io/metaboMisc//reference
   article: https://jasenfinch.github.io/metaboMisc//articles

diff --git a/docs/reference/addAssignments.html b/docs/reference/addAssignments.html
diff --git a/docs/reference/convertSampleInfo.html b/docs/reference/convertSampleInfo.html
diff --git a/docs/reference/detectBatchDiff.html b/docs/reference/detectBatchDiff.html
diff --git a/docs/reference/detectMissInjections.html b/docs/reference/detectMissInjections.html
diff --git a/docs/reference/detectModellingParameters.html b/docs/reference/detectModellingParameters.html