Merge multiple aggDbs

Merge aggdbs, this will generate a new aggdb including all aggregates across provided aggdbs.

mergeAggDbs(object, output, overWrite = FALSE, verbose = TRUE)

Arguments

object

an aggdbList object.

output

Output file name (output will be an aggdb).

overWrite

Should existing output files be overwritten? Defaults to FALSE.

verbose

Should the function be verbose? Defaults to TRUE.

Examples

library(rvatData)
gdb <- create_example_gdb()

# generate two aggregate files
varsetfile <- varSetFile(rvat_example("rvatData_varsetfile.txt.gz"))
aggdb1 <- tempfile()
aggregate(
  x = gdb,
  varSet = getVarSet(varsetfile, unit = c("SOD1", "FUS"), varSetName = "High"),
  maxMAF = 0.001,
  output = aggdb1,
  verbose = FALSE
)

aggdb2 <- tempfile()
aggregate(
  x = gdb,
  varSet = getVarSet(varsetfile, unit = c("NEK1"), varSetName = "High"),
  maxMAF = 0.001,
  output = aggdb2,
  verbose = FALSE
)

# merge using mergeAggDbs
aggdb <- tempfile()
agglist <- aggdbList(c(aggdb1, aggdb2))
mergeAggDbs(
  agglist,
  output = aggdb
)
#> Initializing new aggregate database at: /tmp/RtmpvjdKWE/file153935490a6db
#>   Writing metadata...
#>   Writing analysis parameters...
#>   Writing sample manifest (SM)...
#> Aggregate database initialized successfully.
#> Merging 'file153931e769769'
#> Merging 'file15393de842d7'
#> Merge complete. New aggregate database created at: /tmp/RtmpvjdKWE/file153935490a6db