buildVarSet

Generate optionally weighted variant sets using annotation table(s). See the tutorials for examples. For building varSets directly from the gdb: see buildVarSet-gdb for details
For building varSets interactively from a data.frame seee buildVarSet-data.frame for details

Examples

library(rvatData)

# Build a varSetFile including variants with a moderate predicted impact
gdb <- create_example_gdb()
varsetfile_moderate <- tempfile()
buildVarSet(object = gdb, 
            output = varsetfile_moderate,
            varSetName = "Moderate", 
            unitTable = "varInfo", 
            unitName = "gene_name",
            where = "ModerateImpact = 1")
#> Generated varSetFile: /var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825c54966699
#> varSetFile object
#> Path:/var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825c54966699
#> Units:12

# Build a varSetFile that contains CADD scores
varsetfile_cadd <- tempfile()
buildVarSet(object = gdb, 
            output = varsetfile_cadd,
            varSetName = "CADD", 
            unitTable = "varInfo", 
            unitName = "gene_name",
            weightName = "CADDphred")
#> Generated varSetFile: /var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825c5e29f231
#> varSetFile object
#> Path:/var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825c5e29f231
#> Units:12

# in addition to building a varSetFile from a gdb,
# it can also be build directly from a data.frame
anno <- getAnno(gdb, "varinfo", where = "gene_name in ('SOD1', 'FUS')")
varsetfile_from_df <- tempfile()
buildVarSet(
  anno,
  unitName = "gene_name",
  fields = c("HighImpact"),
  output = varsetfile_from_df
)

# connect to varsetfile and retrieve variant sets
varsetfile <- varSetFile(varsetfile_moderate)
varsets <- getVarSet(varsetfile, unit = c("SOD1", "FUS"))

# see ?getVarSet, ?varSetFile and ?varSetList for more details on connecting and handling varsetfiles.
# see e.g., ?assocTest and ?aggregate for downstream methods that can loop through varsetfiles and varsetlists.