Merge pull request #44 from hugheylab/fix-arrayexpress

fixed processing of arrayexpress data.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: seeker
 Type: Package
 Title: Simplified Fetching and Processing of Microarray and RNA-Seq Data
-Version: 1.1.3
+Version: 1.1.4
 Authors@R: c(
   person('Jake', 'Hughey', , '[email protected]', role = c('aut', 'cre')),
   person('Josh', 'Schoenbachler', , '[email protected]', role = 'aut'))
@@ -51,7 +51,7 @@ Imports:
   withr (>= 2.4.2),
   yaml (>= 2.2.1)
 Suggests:
-  ArrayExpress (>= 1.50.0),
+  ArrayExpress (>= 1.62.0),
   Biobase,
   doParallel (>= 1.0.17),
   knitr,

NEWS.md

@@ -1,3 +1,7 @@
+# seeker 1.1.4
+* Fixed processing of ArrayExpress data (thanks to @jacorvar).
+* Removed deprecated argument from `biomaRt::listEnsemblArchives()`.
+
 # seeker 1.1.3
 * Updated test for fetching metadata again.
 * `fetchMetadata()` now orders its result.

R/array_utils.R

@@ -158,7 +158,7 @@ getNaiveEsetAe = function(study, outputDir, rawDir) {
   # if (metadataOnly) return(list(eset = eset))
 
   if ((platform %in% getPlatforms('cdf')$ae_accession) && hasRaw) {
-    mage = ArrayExpress::getAE(study, path = outputDir, type = 'raw')
+    mage = ArrayExpress::getAE(study, path = outputDir, type = 'full')
     eset = ArrayExpress::ae2bioc(mage)
     rmaOk = TRUE
   } else {
@@ -174,8 +174,8 @@ getNaiveEsetAe = function(study, outputDir, rawDir) {
 
   if (!dir.exists(rawDir)) dir.create(rawDir)
 
-  . = file.rename(file.path(outputDir, mage$rawFiles),
-                  file.path(rawDir, mage$rawFiles))
+  . = file.rename(file.path(outputDir, basename(mage$rawFiles)),
+                  file.path(rawDir, basename(mage$rawFiles)))
 
   return(list(eset = eset, rmaOk = rmaOk))}
 

R/tximport.R

@@ -29,7 +29,7 @@ getTx2gene = function(
   withr::local_options(timeout = 600)
 
   if (is.null(version)) { # let's be strict
-    arch = setDT(biomaRt::listEnsemblArchives(https = TRUE))
+    arch = setDT(biomaRt::listEnsemblArchives())
     version = as.integer(arch[arch$current_release == '*']$version)}
 
   if (!is.null(outputDir)) {

cran-comments.md

@@ -8,17 +8,28 @@
 
 ### R-hub
 
-R-hub builds are giving errors because "Bioconductor does not yet build and check packages for R version 4.4".
+`devtools::check_rhub()`:
 
-See results for [Windows](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-7dd2f5c93e324fceb89b5451f55325ec), [Ubuntu](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-e086fb7a85834001b34f4a6111838921), and [Fedora](https://builder.r-hub.io/status/seeker_1.1.3.tar.gz-c75d4dfc8fd74825b4fbac365d27c862).
+  0 errors ✓ | 0 warnings ✓ | 2 notes ✓
+
+❯ checking for non-standard things in the check directory ... NOTE
+  Found the following files/directories:
+    ''NULL''
+
+❯ checking for detritus in the temp directory ... NOTE
+  Found the following files/directories:
+    'lastMiKTeXException'
+
+See results for [Windows](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-1fd21b320f264289820666012a924a8a), [Ubuntu](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-dd2ecaaf51d24135a360cee4e0b8a858), and [Fedora](https://builder.r-hub.io/status/seeker_1.1.4.tar.gz-6cfb237d17794ae5bd6fa302781fb7b0).
 
 ### GitHub Actions
 
   0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
-See results for Mac, Windows, and Ubuntu [here](https://github.com/hugheylab/seeker/actions/runs/5062969952).
+See results for Mac, Windows, and Ubuntu [here]().
 
 ## Changes from current CRAN release
 
-* Updated test for fetching metadata, this time to make it less sensitive to arbitrary changes on the remote resource.
-* `fetchMetadata()` now orders its result.
+* Fixed processing of ArrayExpress data (thanks to @jacorvar).
+* Removed deprecated argument from `biomaRt::listEnsemblArchives()`.
+* Updated test standards.

inst/extdata/platform_cdf.csv

@@ -14,5 +14,6 @@ pd.mouse430.2,mouse4302mm,A-AFFY-45
 pd.u133.x3p,u133x3phs,A-AFFY-54
 pd.rat230.2,rat2302rn,A-AFFY-43
 pd.hg.u133a,hgu133ahs,A-AFFY-33
+pd.hg.u133.plus.2,hgu133plus2hs,A-AFFY-44
 pd.mogene.1.0.st.v1,mogene10stmm,A-AFFY-130
 pd.mogene.2.0.st,mogene20stmm,A-GEOD-16570