tweak help

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: easylift
 Title: An R package to perform genomic liftover
-Version: 0.99.2
+Version: 0.99.3
 Date: 2023-09-25
 Authors@R: 
     c(

R/easylift.R

@@ -6,8 +6,11 @@
 #' @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.
+#' Can be provided in gzipped or non-gzipped format. If omitted, the function
+#' will look in the default BiocFileCache for a properly named chain file.
+#'
 #' @return A GRanges object with lifted genomic coordinates.
+#' 
 #' @examples
 #' # Lift over the coordinates of the first 10 genes in the hg19 assembly
 #' # to the hg38 assembly
@@ -25,7 +28,7 @@
 #' easylift(gr, "hg38", chain)
 #' 
 #' # To use `BiocFileCache` for the chain file, you can add it to the cache as follows:
-#' # chain_file <- "/path/to/your/chainfile.chain"
+#' # chain_file <- "/path/to/your/hg19ToHg38.over.chain.gz"
 #' # bfc <- BiocFileCache()
 #' # bfcadd(bfc, chain_file)
 #'

README.md

@@ -53,7 +53,7 @@ To use `BiocFileCache` for the chain file, you can add it to the cache
 as follows:
 
 ``` r
-chain_file <- "/path/to/your/chainfile.chain"
+chain_file <- "/path/to/your/hg19ToHg38.over.chain.gz"
 bfc <- BiocFileCache()
 bfcadd(bfc, chain_file)
 ```

vignettes/easylift.Rmd

@@ -10,7 +10,6 @@ author:
   affiliation: 
   - "Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA"
   - "Genetics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA"
-  email: [email protected]
 output: BiocStyle::html_document
 vignette: >
   %\VignetteIndexEntry{Perform Genomic Liftover}
@@ -75,9 +74,11 @@ easylift(gr, to, chain)
 
 ## BiocFileCache
 
-To use `BiocFileCache` for the chain file, you can add it to the cache as follows:
+To use `BiocFileCache` for the chain file, you can add it to the cache
+as follows:
+
 ```{r bioCache, eval=FALSE}
-chain_file <- "/path/to/your/chainfile.chain"
+chain_file <- "/path/to/your/hg19ToHg38.over.chain.gz"
 bfc <- BiocFileCache()
 bfcadd(bfc, chain_file)
 ```
@@ -88,6 +89,10 @@ Then, you can use it in `easylift` like this:
 gr |> easylift("hg38")
 ```
 
+`easylift` here will look for a chain file with the proper name 
+(`genome(gr)` + "To" + Capitalized-`to`-argument + `.over.chain`)
+in the BiocFileCache default location.
+
 # Citation
 
 To cite package ‘easylift’ in publications use: