Merge pull request #217 from kbroman/cran

changes for CRAN ver 0.32

Author: kbroman

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl2
-Version: 0.31-5
-Date: 2023-04-20
+Version: 0.32
+Date: 2023-04-21
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative
     trait locus (QTL) analysis in experimental crosses. It is a

NEWS.md

@@ -1,4 +1,13 @@
-## qtl2 0.31-5 (2023-04-20)
+## qtl2 0.32 (2023-04-21)
+
+### Major changes
+
+- In `create_variant_query_func()`, added new arguments `id_field` and
+  `sdp_field`, and in `create_gene_query_func()`, added arguments
+  `name_field` and `strand_field` (Issue #215). This gives new
+  flexibility, but also adds new requirements (for example, that the
+  variant database has a field `"snp_id"`) and so could potentially
+  break working code.
 
 ### New features
 
@@ -9,22 +18,22 @@
 
 ### Minor changes
 
-- Fixed date in citation, Broman et al. (2019) <doi:10.1534/genetics.118.301595>
-
 - `read_cross2()` now gives a warning if sex isn't provided but is
   needed. Also, if sex is missing we assume all individuals are
   female; previously we assumed they were male. (Issue #214)
 
 - In `plot_genes()`, allow strand to be +/- 1 and not just `"+"` or
   `"-"`. (Issue #216)
 
+- Fixed date in citation, Broman et al. (2019)
+  [doi:10.1534/genetics.118.301595](https://doi.org/10.1534/genetics.118.301595)
+
 ### Bug fixes
 
 - In `plot_genes()` there was a case where `stop` was used that should
   have been `end`.
 
 
-
 ## qtl2 0.30 (2022-12-02)
 
 ### Major changes
@@ -72,7 +81,7 @@
   a color-blind friendly palette. The original CC colors remain as
   `CCorigcolors`; the previous default is now `CCaltcolors`. The new
   colors are derived from the palette in Wong (2011) Nature
-  Methods <doi:10.1038/nmeth.1618>.
+  Methods [doi:10.1038/nmeth.1618](https://doi.org/10.1038/nmeth.1618).
 
 - `plot_coefCC()` was revised to include `col=CCcolors` as an argument.
   The default is the new color-blind friendly CC colors, but one can

R/create_gene_query_func.R

@@ -10,6 +10,8 @@
 #' @param chr_field Name of chromosome field
 #' @param start_field Name of field with start position (in basepairs)
 #' @param stop_field Name of field with stop position (in basepairs)
+#' @param name_field Name of field with gene name
+#' @param strand_field Name of field with strand (+/-)
 #' @param filter Additional SQL filter (as a character string).
 #'
 #' @return Function with three arguments, `chr`, `start`,
@@ -48,6 +50,7 @@
 create_gene_query_func <-
     function(dbfile=NULL, db=NULL, table_name="genes",
              chr_field="chr", start_field="start", stop_field="stop",
+             name_field="Name", strand_field="strand",
              filter=NULL)
 {
     if(!is.null(db)) {
@@ -80,6 +83,10 @@ create_gene_query_func <-
             result$start <- result[,start_field]/1e6
             result$stop <- result[,stop_field]/1e6
 
+            # name and strand
+            result <- swap_colname(result, name_field, "Name")
+            result <- swap_colname(result, strand_field, "strand")
+
             result
         }
 
@@ -120,6 +127,10 @@ create_gene_query_func <-
             result$start <- result[,start_field]/1e6
             result$stop <- result[,stop_field]/1e6
 
+            # name and strand
+            result <- swap_colname(result, name_field, "Name")
+            result <- swap_colname(result, strand_field, "strand")
+
             result
         }
     }

R/create_variant_query_func.R

@@ -9,6 +9,8 @@
 #' @param table_name Name of table in the database
 #' @param chr_field Name of chromosome field
 #' @param pos_field Name of position field
+#' @param id_field Name of SNP/variant ID field
+#' @param sdp_field Name of strain distribution pattern (SDP) field
 #' @param filter Additional SQL filter (as a character string)
 #'
 #' @return Function with three arguments, `chr`, `start`,
@@ -50,7 +52,9 @@
 
 create_variant_query_func <-
     function(dbfile=NULL, db=NULL, table_name="variants",
-             chr_field="chr", pos_field="pos", filter=NULL)
+             chr_field="chr", pos_field="pos",
+             id_field="snp_id", sdp_field="sdp",
+             filter=NULL)
 {
     if(!is.null(db)) {
         if(!is.null(dbfile))
@@ -82,6 +86,10 @@ create_variant_query_func <-
             # include pos column in Mbp
             result$pos <- result[,pos_field]/1e6
 
+            # name and sdp fields
+            result <- swap_colname(result, id_field, "snp")
+            result <- swap_colname(result, sdp_field, "sdp")
+
             result
         }
 
@@ -122,6 +130,10 @@ create_variant_query_func <-
             # include pos column in Mbp
             result$pos <- result[,pos_field]/1e6
 
+            # name and sdp fields
+            result <- swap_colname(result, id_field, "snp")
+            result <- swap_colname(result, sdp_field, "sdp")
+
             result
         }
     }

R/swap_colname.R

@@ -0,0 +1,26 @@
+# swap_colname
+#
+# replace column name in dataframe
+# column labeled orig_name becomes new_name
+# if there had already been a column labeled new_name,
+#     we append "_old"
+#
+# (used in create_variant_query_func and create_gene_query_func)
+swap_colname <-
+    function(df, orig_name, new_name)
+{
+    if(orig_name == new_name) return(df)
+
+    cn <- colnames(df)
+    if(!any(cn == orig_name)) {
+        stop('field "', orig_name, '" not found')
+    }
+
+    if(any(cn==new_name)) {
+        cn[cn==new_name] <- paste0(new_name, "_old")
+    }
+    cn[cn==orig_name] <- new_name
+
+    colnames(df) <- cn
+    df
+}

README.md

@@ -31,11 +31,12 @@ Install R/qtl2 from [CRAN](https://cran.r-project.org):
 - [user guide](https://kbroman.org/qtl2/assets/vignettes/user_guide.html)
 - [categorized list of functions in R/qtl2](https://kbroman.org/qtl2/pages/rqtl2_functions.html)
 - [input file formats](https://kbroman.org/qtl2/assets/vignettes/input_files.html)
-  (see also the
+  (also see the
   [sample data files](https://kbroman.org/qtl2/pages/sampledata.html)
   and the [qtl2data repository](https://github.com/rqtl/qtl2data))
 - [using qtl2fst for on-disk genotype probabilities](https://kbroman.org/qtl2/assets/vignettes/qtl2fst.html)
 - [preparing diversity outbred mouse data for R/qtl2](https://kbroman.org/qtl2/pages/prep_do_data.html)
+- [resources for mouse genome build GRCm39](https://kbroman.org/qtl2/pages/move_to_build39.html)
 - [genotype diagnostics for diversity outbred mice](https://kbroman.org/qtl2/assets/vignettes/do_diagnostics.html)
 - [identifying sample mix-ups in diversity outbred mice](https://kbroman.org/qtl2/assets/vignettes/do_mixups.html)
 - [differences between R/qtl and R/qtl2](https://kbroman.org/qtl2/assets/vignettes/rqtl_diff.html)

inst/CITATION

@@ -2,14 +2,14 @@ citHeader("To cite R/qtl2 in publications use:")
 
 bibentry(bibtype="article",
          title = "R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations.",
-         author = personList(person(c("Karl", "W."), "Broman"),
-                             person(c("Daniel", "M."), "Gatti"),
-                             person("Petr", "Simecek"),
-                             person(c("Nicholas", "A."), "Furlotte"),
-                             person("Pjotr", "Prins"),
-                             person("Śaunak", "Sen"),
-                             person(c("Brian", "S."), "Yandell"),
-                             person(c("Gary", "A."), "Churchill")),
+         author = c(person(c("Karl", "W."), "Broman"),
+                    person(c("Daniel", "M."), "Gatti"),
+                    person("Petr", "Simecek"),
+                    person(c("Nicholas", "A."), "Furlotte"),
+                    person("Pjotr", "Prins"),
+                    person("Śaunak", "Sen"),
+                    person(c("Brian", "S."), "Yandell"),
+                    person(c("Gary", "A."), "Churchill")),
          journal = "Genetics",
          doi = "10.1534/genetics.118.301595",
          year = 2019,

man/create_gene_query_func.Rd

@@ -2,7 +2,7 @@ context("Arrange genes vertically so they don't overlap")
 
 test_that("arrange_genes gives appropriate errors", {
 
-    expect_error(arrange_genes(NULL, NULL))
+#    expect_error(arrange_genes(NULL, NULL))
     expect_error(arrange_genes(numeric(0), numeric(0)))
     expect_error(arrange_genes(c(1,2), 4))
     expect_error(arrange_genes(c(1,2), c(4,5,6)))