Collapse multiple aggregate files

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

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

Arguments

object

an aggregateFileList object.

output

Output file name (output will be gz compressed text). 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)

# collapse aggregatefiles
aggregatefile <- tempfile()
collapseAggregateFiles(
  aggregateFileList(c(aggregatefile1, aggregatefile2)),
  output = aggregatefile
)
#> 1/2
#> 2/2
aggregates <- read.table(aggregatefile, 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