buildVarSet-data.frame — buildVarSet-data.frame • rvat

Generate optionally weighted variant sets using annotation table(s). See the tutorials for examples.

# S4 method for data.frame
buildVarSet(
  object,
  unitName,
  fields,
  output = NULL,
  memlimit = NULL,
  mask = TRUE
)

Arguments

object: A data.frame containing variant annotations
unitName: Field to utilize for aggregation unit names.
fields: Which fields in the data.frame to use as variant annotations. These fields can be 1) an indicator (0,1 or FALSE/TRUE) that flags variants with the annotation, e.g. a column named 'LOF' that indicates whether the variant is predicted to lead to loss-of-function.; or 2) variant weights, e.g. a column named 'CADD' that contains CADD scores. Multiple fields can be specified, which will result in multiple rows per aggregation unit in the resulting varSetFile.
output: Optional output file name (output will be gz compressed text).
memlimit: Defaults to NULL, currently not implemented.
mask: If the annotation field is a 0,1 or FALSE/TRUE indicator, should variants with 0/FALSE be dropped? Defaults to TRUE. If FALSE, all variants will be included, and will be assigned weights 0 and 1.

Examples


library(rvatData)

gdb <- create_example_gdb()
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_from_df)
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.