Class to facilitate merging aggregateFiles

Class to facilitate merging aggregateFiles. By providing a vector of aggregateFile filepaths, aggregateFileList will check whether identical samples are included and if duplicated units are included. The aggregateFileList can then be used to merge the aggregateFiles into either a new aggregateFile, or merge all included aggregates into a single aggregate score per sample (mergeAggregateFiles).

Initialize an aggregateFileList object

• aggregateFileList(filelist, checkDups=TRUE): Here filelist is a vector of aggregateFile filepaths. checkDups is set to TRUE by default, in which case an error raised if unit names are duplicated across aggregateFiles.

Getters

In the following code snippets, x is an aggregateFileList object.

• listUnits(x): Return a vector of all units included across aggregateFiles in the aggregateFileList.

• listSamples(x): Return a vector of all samples included across aggregateFiles in the aggregateFileList.

Merge or collapse aggregateFiles

• mergeAggregateFiles(object, output = NULL, verbose = TRUE): Merge aggregrateFiles, this will generate a new aggregateFile including all aggregates across provided aggregateFiles. See mergeAggregateFiles for details.

• collapseAggregateFiles(object, output = NULL, verbose = TRUE): 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. See collapseAggregateFiles for details.

See also

mergeAggregateFiles

collapseAggregateFiles

assocTest-aggregateFile

aggregate

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