v0.99.16 -- switch to importing functions in txdbmaker that used to b…

…e in GenomicFeatures

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: GenomicState
 Title: Build and access GenomicState objects for use with derfinder tools from
     sources like Gencode
-Version: 0.99.15
-Date: 2021-08-09
+Version: 0.99.16
+Date: 2024-12-12
 Authors@R: 
     person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 
     email = "[email protected]", comment = c(ORCID = "0000-0003-2140-308X"))
@@ -22,9 +22,10 @@ Imports:
     IRanges,
     org.Hs.eg.db,
     utils,
-    methods
+    methods,
+    txdbmaker
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -8,3 +8,4 @@ export(gencode_txdb)
 export(local_metadata)
 import(AnnotationHub)
 importFrom(methods,is)
+importFrom(txdbmaker,makeTxDbFromGFF)

R/gencode_txdb.R

@@ -13,6 +13,7 @@
 #'
 #' @return A [GenomicFeatures::TxDb-class] object.
 #' @export
+#' @importFrom txdbmaker makeTxDbFromGFF
 #' @author Leonardo Collado-Torres
 #' @references Based on code for the `brainflowprobes` package at:
 #' <https://github.com/LieberInstitute/brainflowprobes/blob/devel/data-raw/create_sysdata.R>
@@ -52,7 +53,7 @@ gencode_txdb <- function(
     # gencode_txdb("31", "hg19", chrs = "chr21")
     ## though it works with
     # gencode_txdb("31", "hg18")
-    # txdb <- GenomicFeatures::makeTxDbFromGFF(
+    # txdb <- txdbmaker::makeTxDbFromGFF(
     #     gtf_file,
     #     organism = 'Homo sapiens',
     #     chrominfo = GenomeInfoDb::Seqinfo(genome = genome)
@@ -71,21 +72,21 @@ gencode_txdb <- function(
     )
 
     # message(paste(Sys.time(), "preparing metadata"))
-    metadata <- GenomicFeatures:::.prepareGFFMetadata(
+    metadata <- txdbmaker:::.prepareGFFMetadata(
         file = gtf_file,
         dataSource = NA, organism = "Homo sapiens",
         taxonomyId = NA, miRBaseBuild = NA, metadata = NULL
     )
 
     message(paste(Sys.time(), "building the txdb object"))
-    gr <- GenomicFeatures:::.tidy_seqinfo(
+    gr <- txdbmaker:::.tidy_seqinfo(
         gr = gencode_gtf,
         chrominfo = GenomeInfoDb::Seqinfo(genome = genome)
     )
 
     ## Prune again since GenomeInfoDb::Seqinfo() will return many seqlevels
     gr <- GenomeInfoDb::keepSeqlevels(gr, chrs, pruning.mode = "coarse")
-    txdb <- GenomicFeatures::makeTxDbFromGRanges(gr, metadata = metadata)
+    txdb <- txdbmaker::makeTxDbFromGRanges(gr, metadata = metadata)
     return(txdb)
 }
 

vignettes/GenomicState.Rmd

@@ -60,7 +60,8 @@ bib <- c(
     glue = citation("glue")[1],
     AnnotationHub = citation("AnnotationHub")[1],
     AnnotationHubData = citation("AnnotationHubData")[1],
-    GenomicRanges = citation("GenomicRanges")[1]
+    GenomicRanges = citation("GenomicRanges")[1],
+	txdbmaker = citation("txdbmaker")[1]
 )
 ```
 
@@ -332,6 +333,7 @@ The `r Biocpkg('GenomicState')` package `r Citep(bib[['GenomicState']])` was mad
 * `r Biocpkg('AnnotationHub')` `r Citep(bib[['AnnotationHub']])`
 * `r Biocpkg('AnnotationHubData')` `r Citep(bib[['AnnotationHubData']])`
 * `r Biocpkg('GenomicRanges')` `r Citep(bib[['GenomicRanges']])`
+* `r Biocpkg('txdbmaker')` `r Citep(bib[['txdbmaker']])`
 
 Code for creating the vignette