push fixes

Author: bschilder

.github/workflows/check-bioc-docker.yml

@@ -94,15 +94,15 @@ jobs:
       # which is only available with Linux as the OS.
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -362,7 +362,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         with:
           name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: echoLD
 Type: Package
 Title: echoverse module: LD downloading and processing
-Version: 0.99.7
+Version: 0.99.8
 Authors@R: 
     c(person(given = "Brian",
            family = "Schilder",
@@ -31,12 +31,12 @@ Imports:
     echotabix,
     downloadR,
     echodata,
+    echoconda,
     dplyr,
     methods,
     Matrix,
     data.table,  
-    reticulate,  
-    GenomeInfoDb,  
+    reticulate,
     GenomicRanges,
     VariantAnnotation,
     snpStats,
@@ -58,7 +58,8 @@ Suggests:
 Remotes:
     github::RajLabMSSM/echotabix,
     github::RajLabMSSM/downloadR,
-    github::RajLabMSSM/echodata
+    github::RajLabMSSM/echodata,
+    github::RajLabMSSM/echoconda
 RoxygenNote: 7.2.1.9000
 VignetteBuilder: knitr
 License: GPL (>= 3)

NAMESPACE

@@ -5,7 +5,7 @@ export(get_LD)
 export(get_LD_blocks)
 export(get_LD_matrix)
 export(get_LD_vcf)
-export(get_UKB_MAF)
+export(get_MAF_UKB)
 export(get_lead_r2)
 export(plot_LD)
 export(r2_to_r)
@@ -24,7 +24,6 @@ importFrom(data.table,fread)
 importFrom(data.table,merge.data.table)
 importFrom(downloadR,downloader)
 importFrom(downloadR,load_rdata)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
 importFrom(dplyr,rename)

NEWS.md

@@ -1,3 +1,22 @@
+# echoLD 0.99.8
+
+## New features 
+
+* `get_UKB_MAF` --> `get_MAF_UKB`
+* `get_LD_UKB`:
+    - New subfunction `load_ld_r``tryFun`: 
+    - Remove `tryFun` function. 
+
+## Bug fixes
+
+* Added `echoconda` to *Remotes*: `github::RajLabMSSM/echoconda`
+* Remote `GenomeInfoDb` Import (no longer used here).  
+* Fix GHA: @master --> @v2  
+* Fix `saveSparse` example. 
+* Fix `filter_LD` unit test. 
+* Fix `download_UKB_LD`: Update `downloadR::downloader` arg 
+    from `output_path` --> `output_dir` 
+
 # echoLD 0.99.7
 
 ## New features

R/download_UKB_LD.R

@@ -29,7 +29,7 @@ download_UKB_LD <- function(LD.prefixes,
             out.file <- downloadR::downloader(
                 input_url = furl,
                 download_method = download_method,
-                output_path = file.path(locus_dir, "LD"),
+                output_dir = file.path(locus_dir, "LD"),
                 background = background,
                 conda_env = conda_env,
                 nThread = nThread,

R/get_LD.R

@@ -87,8 +87,8 @@ get_LD <- function(query_dat,
                    conda_env = "echoR_mini",
                    nThread = 1) {
 
-    # echoverseTemplate:::source_all(); 
-    # echoverseTemplate:::args2vars(get_LD)
+    # echoverseTemplate:::source_all();
+    # echoverseTemplate:::args2vars(echoLD:::get_LD)
 
     LD_reference <- LD_reference[1]
     LD_ref_type <- LD_reference_options(LD_reference = LD_reference, 
@@ -109,7 +109,7 @@ get_LD <- function(query_dat,
         LD_list <- read_LD_list(LD_path=RDS_path,
                                 query_dat=query_dat,
                                 verbose=verbose)
-    } else if (LD_ref_type == "ukb") {
+    } else if (LD_ref_type=="ukb") {
         #### UK Biobank ####
         LD_list <- get_LD_UKB(
             query_dat = query_dat,

R/get_LD_1KG.R

@@ -27,7 +27,7 @@ get_LD_1KG <- function(locus_dir,
                        local_storage = NULL,
                        leadSNP_LD_block = FALSE,
                        force_new = FALSE,
-                       force_new_MAF = FALSE,
+                       force_new_maf = FALSE,
                        fillNA = 0,
                        stats = "R",
                        as_sparse = TRUE,
@@ -65,7 +65,7 @@ get_LD_1KG <- function(locus_dir,
     query_dat <- snpstats_get_MAF(
         query_dat = query_dat,
         ss = ss,
-        force_new_MAF = force_new_MAF,
+        force_new_maf = force_new_maf,
         verbose = verbose
     )
     #### Filter out SNPs not in the same LD block as the lead SNP ####

R/get_LD_UKB.R

@@ -133,15 +133,9 @@ get_LD_UKB <- function(query_dat,
             URL <- paste(URL, LD.prefixes, sep="/")
             messager("Importing UKB LD file directly to R from:",v = verbose)
         } 
-        #### Import LD via python function #### 
-        reticulate::source_python(
-            system.file("tools", "load_ld.py",package = "echoLD"
-        ))
-        messager("load_ld() python function input:",URL,v = verbose)
-        messager("Reading LD matrix into memory.",
-                 "This could take some time...",v = verbose)
-        server <- FALSE
-        ld.out <- tryFunc(input = URL, load_ld, server)
+        #### Import LD via python function ####  
+        ld.out <- load_ld_r(URL=URL,
+                            verbose=verbose) 
         #### LD matrix: as matrix ####
         ld_R <- ld.out[[1]]
         messager("+ Full UKB LD matrix:",
@@ -161,7 +155,7 @@ get_LD_UKB <- function(query_dat,
         if (is.null(colnames(ld_R))) colnames(ld_R) <- ld_snps$rsid
         #### As a last resort download UKB MAF ####
         if (!"MAF" %in% colnames(query_dat)) { 
-           query_dat<- get_UKB_MAF(
+           query_dat<- get_MAF_UKB(
                query_dat = query_dat,  
                 nThread = nThread,
                 download_method = download_method,

R/get_LD_vcf.R

@@ -7,6 +7,7 @@
 #' @param fillNA When pairwise LD between two SNPs is \code{NA},
 #' replace with 0.
 #' @inheritParams get_LD
+#' @inheritParams get_MAF_UKB
 #' @inheritParams echotabix::query_vcf
 #' @inheritParams echotabix::query
 #' @inheritParams snpStats::ld
@@ -36,7 +37,7 @@ get_LD_vcf <- function(locus_dir = tempdir(),
                        overlapping_only = TRUE,
                        leadSNP_LD_block = FALSE,
                        force_new = FALSE,
-                       force_new_MAF = FALSE,
+                       force_new_maf = FALSE,
                        fillNA = 0,
                        stats = "R",
                        as_sparse = TRUE,
@@ -71,7 +72,7 @@ get_LD_vcf <- function(locus_dir = tempdir(),
     query_dat <- snpstats_get_MAF(
         query_dat = query_dat,
         ss = ss,
-        force_new_MAF = force_new_MAF,
+        force_new_maf = force_new_maf,
         verbose = verbose
     )
     #### Filter out SNPs not in the same LD block as the lead SNP ####

R/get_UKB_MAF.R renamed to R/get_MAF_UKB.R

@@ -4,7 +4,7 @@
 #' download MAF from UK Biobank and use that instead.
 #'
 #' @param query_dat SNP-level data.
-#' @param output_path Path to store UKB_MAF file in.
+#' @param output_dir Path to store UKB_MAF file in.
 #' @param force_new_maf Download UKB_MAF file again.
 #' @param verbose Print messages.
 #' @inheritParams downloadR::downloader
@@ -13,17 +13,17 @@
 #' @source \href{http://biobank.ctsu.ox.ac.uk/showcase/field.cgi?id=22801}{UKB}
 #' @export
 #' @importFrom data.table fread merge.data.table data.table
-#' @importFrom dplyr %>% group_by slice rename
+#' @importFrom dplyr group_by slice rename
 #' @importFrom tools R_user_dir
 #' @importFrom downloadR downloader
 #' 
 #' @examples
 #' query_dat<- echodata::BST1
 #' query_dat$MAF <- NULL
-#' dat2 <- echoLD::get_UKB_MAF(query_dat = query_dat)
-get_UKB_MAF <- function(query_dat,
-                        output_path = tools::R_user_dir(package = "echoLD",
-                                                        which = "cache"),
+#' dat2 <- echoLD::get_MAF_UKB(query_dat = query_dat)
+get_MAF_UKB <- function(query_dat,
+                        output_dir = tools::R_user_dir(package = "echoLD",
+                                                       which = "cache"),
                         force_new_maf = FALSE,
                         download_method = "axel",
                         nThread = 1,
@@ -41,10 +41,10 @@ get_UKB_MAF <- function(query_dat,
         ),
         chrom, "_v3.txt"
     )
-    out_file <- file.path(output_path, basename(input_url))
+    out_file <- file.path(output_dir, basename(input_url))
     if (file.exists(out_file)) {
         if (file.size(out_file) == 0) {
-            messager("+ UKB MAF:: Removing empty UKB MAF ref file.")
+            messager("+ UKB MAF:: Removing empty UKB MAF ref file.",v=verbose)
             file.remove(out_file)
         }
     }
@@ -53,7 +53,7 @@ get_UKB_MAF <- function(query_dat,
     } else {
         out_file <- downloadR::downloader(
             input_url = input_url,
-            output_path = output_path,
+            output_dir = output_dir,
             background = FALSE,
             force_overwrite = force_new_maf,
             download_method = download_method,
@@ -76,10 +76,10 @@ get_UKB_MAF <- function(query_dat,
     }
     merged_dat <- data.table::merge.data.table(query_dat, maf,
         by = "POS"
-    ) %>%
+    ) |>
         # Make sure each SNP just appears once
-        dplyr::group_by(SNP) %>%
-        dplyr::slice(1) %>%
+        dplyr::group_by(SNP) |>
+        dplyr::slice(1) |>
         data.table::data.table()
     return(merged_dat)
 }