update dt_to_granges to avoid using SEQnames unless neccessary

RajLabMSSM · Nov 17, 2023 · 4c36de7 · 4c36de7
1 parent 9a39ba3
commit 4c36de7
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Showing 3 changed files with 12 additions and 6 deletions.
diff --git a/R/dt_to_granges.R b/R/dt_to_granges.R
@@ -13,6 +13,7 @@
 #' 
 #' @family utils
 #' @export
+#' @import data.table
 #' @examples 
 #' gr <- echodata::dt_to_granges(dat = echodata::BST1)
 dt_to_granges <- function(dat,
@@ -23,15 +24,20 @@ dt_to_granges <- function(dat,
                           verbose = TRUE) {
     requireNamespace("GenomicRanges")
     requireNamespace("GenomeInfoDb")
+
+
     if (is_granges(dat)) {
         messager("dat is already a GRanges object.", v = verbose)
         gr.snp <- dat
     } else {
         messager("Converting dat to GRanges object.", v = verbose)
-        dat[["SEQnames"]] <- dat[[chrom_col]]
+        dat <- data.table::as.data.table(dat)
+        if(chrom_col=="seqnames"){
+            data.table::setnames(dat,"seqnames","SEQnames")
+        } 
         gr.snp <- GenomicRanges::makeGRangesFromDataFrame(
             dat,
-            seqnames.field = "SEQnames",
+            seqnames.field = chrom_col,
             start.field = start_col,
             end.field = end_col,
             keep.extra.columns = TRUE

diff --git a/man/reassign_lead_snps.Rd b/man/reassign_lead_snps.Rd
diff --git a/tests/testthat/test-dt_to_granges.R b/tests/testthat/test-dt_to_granges.R
@@ -7,7 +7,7 @@ test_that("dt_to_granges works", {
     testthat::expect_true(
         all.equal(
             colnames(GenomicRanges::mcols(gr)),
-            colnames(dat)[colnames(dat)!="POS"]
+            colnames(dat)[!colnames(dat)%in% c("CHR","POS")]
             )
         )
 
@@ -18,7 +18,7 @@ test_that("dt_to_granges works", {
     testthat::expect_true(
       all.equal(
         colnames(GenomicRanges::mcols(gr2)),
-        colnames(dat)[colnames(dat)!="POS"]
+        colnames(dat)[!colnames(dat)%in% c("CHR","POS")]
       )
     ) 
 })