From ef48e84d5070a950ac885fd73ba5dcc259a3294d Mon Sep 17 00:00:00 2001
From: mikelove <michaelisaiahlove@gmail.com>
Date: Fri, 11 Aug 2023 18:51:18 -0400
Subject: [PATCH] fixing up some things

---
 R/easylift.R    | 16 ++++++++--------
 man/easylift.Rd |  4 ++--
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/R/easylift.R b/R/easylift.R
index b5cef28..62e9ba8 100644
--- a/R/easylift.R
+++ b/R/easylift.R
@@ -3,7 +3,7 @@
 #' This function takes a GRanges object with genomic coordinates in one genome
 #' assembly and lifts them to another genome assembly using a chain file.
 #'
-#' @param gr A GRanges object with genomic coordinates in the original assembly.
+#' @param x A GRanges object with genomic coordinates in the original assembly.
 #' @param to The target genome assembly (e.g., "hg38").
 #' @param chain The path to the chain file containing the liftover mapping.
 #' Can be provided in gzipped or non-gzipped format.
@@ -14,21 +14,21 @@
 #' @import tools
 #' @import BiocFileCache
 #' @export
-easylift <- function(gr, to, chain) {
-  if (is.na(GenomeInfoDb::genome(gr))) {
+easylift <- function(x, to, chain) {
+  if (any(is.na(GenomeInfoDb::genome(x)))) {
     stop(
-      "The genome information for the 'gr' object is missing (NA). Please set the genome before using easylift."
+      "The genome information is missing. Please set genome(x) before using easylift."
     )
   }
   # Convert the input GRanges to the "UCSC" seqlevels style if not already
-  if (GenomeInfoDb::seqlevelsStyle(gr) != "UCSC") {
-    GenomeInfoDb::seqlevelsStyle(gr) <- "UCSC"
+  if (GenomeInfoDb::seqlevelsStyle(x) != "UCSC") {
+    GenomeInfoDb::seqlevelsStyle(x) <- "UCSC"
   }
 
   if (missing(chain)) {
     bfc <- BiocFileCache()
     capTo <- paste0(toupper(substr(to,1,1)),substr(to,2,nchar(to))) # capitalize first letter
-    trychainfile <- paste0(genome(gr),"To",capTo,".over.chain")
+    trychainfile <- paste0(genome(x),"To",capTo,".over.chain")
     q <- bfcquery(bfc, trychainfile)
     if (nrow(q) >= 1) {
       chain <- bfc[[q$rid[1]]]
@@ -57,7 +57,7 @@ easylift <- function(gr, to, chain) {
   }
 
   # LiftOver the genomic coordinates
-  cur <- unlist(rtracklayer::liftOver(gr, ch))
+  cur <- unlist(rtracklayer::liftOver(x, ch))
 
   GenomeInfoDb::seqlevels(cur) <- GenomeInfoDb::seqlevels(to_seqinfo)
   GenomeInfoDb::seqinfo(cur) <- to_seqinfo
diff --git a/man/easylift.Rd b/man/easylift.Rd
index e8413ca..9d7ad77 100644
--- a/man/easylift.Rd
+++ b/man/easylift.Rd
@@ -4,10 +4,10 @@
 \alias{easylift}
 \title{Lift genomic coordinates from one genome assembly to another.}
 \usage{
-easylift(gr, to, chain)
+easylift(x, to, chain)
 }
 \arguments{
-\item{gr}{A GRanges object with genomic coordinates in the original assembly.}
+\item{x}{A GRanges object with genomic coordinates in the original assembly.}
 
 \item{to}{The target genome assembly (e.g., "hg38").}