Merge pull request #35 from vyepez88/code_cleaning

Code cleaning

.travis.yml

@@ -43,7 +43,7 @@ addons:
 install:
   - cd $DROP_DIR
   - R -e "if ('FRASER' %in% rownames(installed.packages())) remove.packages('FRASER')"
-  - R -e "install.packages('BiocManager'); BiocManager::install('remotes'); BiocManager::install('gagneurlab/FRASER', ref = 'R3.6')"
+  - R -e "install.packages('BiocManager'); BiocManager::install('remotes'); BiocManager::install('gagneurlab/FRASER')"
 #  - R -e "if ('tMAE' %in% rownames(installed.packages())) remove.packages('tMAE')"
   - Rscript travis/installRPackages.R drop/requirementsR.txt
   - bash travis/install_bcftools.sh

drop/configHelper.py

@@ -124,6 +124,7 @@ def setDefaults(self, config, method=None):
             setKey(config, ["aberrantExpression"], "groups", None, verbose=VERBOSE)
             setKey(config, ["aberrantExpression"], "padjCutoff", .05, verbose=VERBOSE)
             setKey(config, ["aberrantExpression"], "zScoreCutoff", 0, verbose=VERBOSE)
+            setKey(config, ["aberrantSplicing"], "maxTestedDimensionProportion", 3, verbose=VERBOSE)
 
         # aberrant splicing
         if self.method == "AS" or self.method is None:
@@ -138,6 +139,7 @@ def setDefaults(self, config, method=None):
             setKey(config, ["aberrantSplicing"], "padjCutoff", 0.05, verbose=VERBOSE)
             setKey(config, ["aberrantSplicing"], "zScoreCutoff", 0.05, verbose=VERBOSE)
             setKey(config, ["aberrantSplicing"], "deltaPsiCutoff", 0.05, verbose=VERBOSE)
+            setKey(config, ["aberrantSplicing"], "maxTestedDimensionProportion", 6, verbose=VERBOSE)
 
         # monoallelic expression
         if self.method == "MAE" or self.method is None:
@@ -219,7 +221,7 @@ def createSampleFileMapping(self, sample_annotation):
 
     def createGroupIds(self, group_key="DROP_GROUP", file_type="RNA_BAM_FILE", sep=','):
         """
-        Create a full and filtered list of RNA assay IDs subsetted by specified OUTRIDER groups
+        Create a full and filtered list of RNA assay IDs subsetted by specified DROP groups
         """
         sa = self.sample_annotation
         sf = self.sample_file_mapping
@@ -301,7 +303,7 @@ def checkFileExists(self, sampleID, file_type, verbose=True):
 
     def getFilePath(self, sampleId, file_type):
         """
-        Function for getting the file path given the sampleId and file t
+        Function for getting the file path given the sampleId and file type
         sampleId: ID of sample
         file_type: e.g. "RNA_BAM_FILE", "DNA_VCF_FILE"
         """

drop/template/Scripts/AberrantSplicingAnalysis/Overview.R

@@ -79,7 +79,7 @@ fraser_links <- get_html_path(datasets = datasets,
 #'
 #' ## Analyze individual results
 # Read the first fds object and results table
-fds <- loadFraseRDataSet(file = snakemake@params$fds_files[[1]])
+fds <- loadFraserDataSet(file = snakemake@params$fds_files[[1]])
 res <- fread(snakemake@params$result_tables[[1]])
 
 #' Display the results table of the first dataset

drop/template/config.yaml

@@ -23,7 +23,8 @@ aberrantExpression:
     fpkmCutoff: 1
     implementation: autoencoder
     padjCutoff: 0.05
-    zscoreCutoff: 0
+    zScoreCutoff: 0
+    maxTestedDimensionProportion: 3
 
 aberrantSplicing:
     groups:
@@ -37,6 +38,7 @@ aberrantSplicing:
     padjCutoff: 0.05
     zScoreCutoff: 0
     deltaPsiCutoff: 0.3
+    maxTestedDimensionProportion: 6
 
 mae:
     groups:
@@ -51,7 +53,7 @@ mae:
     maxAF: .001
     # VCF-BAM matching
     qcVcf:        # path to common variant file e.g. qc_vcf_1000G.vcf.gz
-    qcGroup: mae
+    qcGroups: mae
 
 tools:
     gatkCmd: gatk