Collapse multiple aggDbs

Collapse aggDbs by aggregating values across aggdbs. This will result in one aggregate score for each sample, representing the aggregate value across aggregate dbs. The output will be a two-column matrix including sample IDs and aggregate scores respectively.

collapseAggDbs(object, output = NULL, overWrite = FALSE, verbose = TRUE)

Arguments

object

an aggdbList object.

output

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

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
)

# collapse aggdbs
aggdb <- tempfile()
collapseAggDbs(
  aggdbList(c(aggdb1, aggdb2)),
  output = aggdb
)
#> Processing aggdb 1/2: 'file1539345db0349'
#> Processing aggdb 2/2: 'file153937c458732'
#> Writing merged aggregates to: /tmp/RtmpvjdKWE/file153935fc07379
aggregates <- read.table(aggdb, header = TRUE)
head(aggregates)
#>    IID    aggregate
#> 1 ALS1 0.0000000000
#> 2 ALS2 0.0010542500
#> 3 ALS3 0.0002103009
#> 4 ALS4 0.0000000000
#> 5 ALS5 0.0000000000
#> 6 ALS6 0.0000851209