Re-format code automatically

LieberInstitute · Mar 27, 2024 · 2a82ae5 · 2a82ae5
1 parent 87234fc
commit 2a82ae5
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Showing 4 changed files with 18 additions and 12 deletions.
diff --git a/R/corner.R b/R/corner.R
@@ -19,12 +19,14 @@
 #' corner(lis)
 corner <- function(mat, n = 6) {
     types <-
-        c("list",
+        c(
+            "list",
             "DataFrame",
             "data.frame",
             "GRanges",
             "matrix",
-            "tbl_df")
+            "tbl_df"
+        )
     if (!(class(mat)[1] %in% types)) {
         stop(
             "The class of your object (",
@@ -35,8 +37,9 @@ corner <- function(mat, n = 6) {
     }
     if (class(mat)[1] == "list") {
         # return corners of first n items of list
-        return(lapply(mat[seq_len(min(length(mat), n))], function(x)
-            x[seq_len(min(nrow(x), n)), seq_len(min(ncol(x), n))]))
+        return(lapply(mat[seq_len(min(length(mat), n))], function(x) {
+            x[seq_len(min(nrow(x), n)), seq_len(min(ncol(x), n))]
+        }))
     } else {
         return(mat[seq_len(min(nrow(mat), n)), seq_len(min(ncol(mat), n))])
     }

diff --git a/R/expression_cutoff.R b/R/expression_cutoff.R
@@ -64,8 +64,9 @@
 #'
 #' ## View the pdf with the following code
 #' utils::browseURL("test_expression_cutoff.pdf")
-expression_cutoff <- function(expr, max_cut = 1, seed = NULL, n.boot = 2000,
-    k = 2) {
+expression_cutoff <- function(
+        expr, max_cut = 1, seed = NULL, n.boot = 2000,
+        k = 2) {
     meanExpr <- rowMeans(expr)
 
 

diff --git a/R/junctionCount.R b/R/junctionCount.R
@@ -36,10 +36,11 @@
 #' ## TODO (need some data)
 #' ## See https://github.com/LieberInstitute/RNAseq-pipeline/blob/ab71dedb36bcc3dad57233e645fabd5deb96d446/sh/create_count_objects-human.R#L633-L643
 #' ## for an example of how it's being using the the RNA-seq pipeline code
-junctionCount <- function(junctionFiles, sampleNames = names(junctionFiles),
-    output = c("Count", "Rail"), minOverhang = 0,
-    strandSpecific = FALSE, illuminaStranded = FALSE,
-    minCount = 1, maxCores = 1, skipLines = ifelse(output == "Count", 0, 1)) {
+junctionCount <- function(
+        junctionFiles, sampleNames = names(junctionFiles),
+        output = c("Count", "Rail"), minOverhang = 0,
+        strandSpecific = FALSE, illuminaStranded = FALSE,
+        minCount = 1, maxCores = 1, skipLines = ifelse(output == "Count", 0, 1)) {
     stopifnot(length(junctionFiles) == length(sampleNames))
     stopifnot(output %in% c("Count", "Rail"))
 

diff --git a/R/lab_presenters.R b/R/lab_presenters.R
@@ -45,8 +45,9 @@
 #'     ## If it's a new sheet, we recommend sharing an editable link so other
 #'     ## lab members can swap out as necessary.
 #' }
-lab_presenters <- function(presenters, start_date = "2019-09-18",
-    sheet_name = "Jaffelab research presenters", n = 2, repeat_day = 7) {
+lab_presenters <- function(
+        presenters, start_date = "2019-09-18",
+        sheet_name = "Jaffelab research presenters", n = 2, repeat_day = 7) {
     ## Check inputs
     if (!is.character(presenters)) {
         stop("'presenters' should be a character vector.", call. = FALSE)