Merge multiple aggregate files

Merge aggregrateFiles, this will generate a new aggregateFile including all aggregates across provided aggregateFiles.

mergeAggregateFiles(object, output = NULL, verbose = TRUE)

Arguments

object

an aggregateFileList object.

output

Output file name (output will be an aggregateFile). Defaults to NULL, in which case a data.frame will be returned.

verbose

Should the function be verbose? Defaults to TRUE.

Examples

library(rvatData)
gdb <- gdb(rvat_example("rvatData.gdb"))

# generate two aggregate files
varsetfile <- varSetFile(rvat_example("rvatData_varsetfile.txt.gz"))
aggregatefile1 <- tempfile()
aggregate(x = gdb,
          varSet = getVarSet(varsetfile, unit = c("SOD1", "FUS"), varSetName = "High"),
          maxMAF = 0.001,
          output = aggregatefile1,
          verbose = FALSE)

aggregatefile2 <- tempfile()
aggregate(x = gdb,
          varSet = getVarSet(varsetfile, unit = c("NEK1"), varSetName = "High"),
          maxMAF = 0.001,
          output = aggregatefile2,
          verbose = FALSE)

# merge using mergeAggregateFiles
aggregatefile <- tempfile()
agglist <- aggregateFileList(c(aggregatefile1, aggregatefile2))
mergeAggregateFiles(
  agglist,
  output = aggregatefile
  )
#> 1/2
#> 2/2