API for dbottomly/oligoMask
Tools for masking out problematic Affymetrix probes using VCF files and the oligo package

Global functions
SangerTableSchemaList Man page Source code
SunGeneFS Man page
TableSchemaList Man page
TableSchemaList-class Man page
VariantMaskParams Man page Source code
VariantMaskParams-class Man page
VcfDB Man page
VcfDB-class Man page
add.status.probe.info Source code
add.vcf.to.db Man page
check.and.add.tables Source code
closeDb Source code
create.sanger.mouse.vcf.db Man page Source code
createTable Man page
createTable,TableSchemaList-method Man page
default.search.cols Source code
default.tab.list Source code
dict.to.where Source code
filter.sanger.vcf Source code
get.shortest.query.path Source code
getDb Source code
getProbeDf Man page
getProbeDf,VariantMaskParams-method Man page
granges.to.dta Source code
guess.query.func Source code
initDbConnection Source code
insertStatement Man page
insertStatement,TableSchemaList-method Man page
make.allele.dta Source code
make.genotype.dta Source code
make.probe.to.snp Source code
make.ref.dta Source code
make.vcf.table Man page Source code
maskDb Man page
maskDb,VariantMaskParams-method Man page
maskRMA Man page
maskRMA,GeneFeatureSet-method Man page
mergeStatement Man page
mergeStatement,TableSchemaList-method Man page
oligoMask Man page
oligoMask-package Man page
om.db.file Man page Source code
om.lo.file Man page Source code
om.tab.file Man page Source code
om.vcf.file Man page Source code
onAttach Source code
onUnload Source code
populate.db.tbl.schema.list Man page Source code
return.element Source code
run.analysis.strand Source code
searchCols Man page
searchCols,TableSchemaList-method Man page
searchDict Man page
searchDict,TableSchemaList-method Man page
searchTables Man page
searchTables,TableSchemaList-method Man page
tbsl Man page
tbsl,VcfDB-method Man page
test.pd.1.0.st.v1 Man page
tsl.to.graphNEL Source code
valid.TableSchemaList Source code
valid.VariantMaskParams Source code
validProbeQuery Man page
validProbeQuery,VariantMaskParams-method Man page
vcfDb Man page
vcfDb,VcfDB-method Man page
dbottomly/oligoMask documentation built on May 12, 2017, 9:05 p.m.