Class to manage interactions with an aggregateFile

The aggregate method saves genotypes aggregates compressed on disk. The aggregateFile class manages connecting/interacting with these files and retrieving units of interest.

Build an aggregateFile

• aggregate(x, ...): Returns an aggregate of genotypes for each individual. See aggregate() for details.

Connect to an aggregateFile

• aggregateFile(path): Connect to an aggregateFile object.

Getters

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

• getUnit(x, unit): Retrieve aggregates for specified unit(s). Use listUnits(x) to list the units includes in the aggregateFile Output will be a matrix.

• listUnits(x): Return a vector of all units included in the aggregateFile

• listSamples(x): Return a vector of all sample IDs included in the aggregateFile

Association testing

An aggregateFile can be directly supplied to the assocTest() method.

Merging

Aggregate files can be merged using the mergeAggregateFiles method.

See also

mergeAggregateFiles

aggregateFileList

assocTest-aggregateFile

aggregate

Examples

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

# generate the aggregates based on a varSetFile
varsetfile <- varSetFile(rvat_example("rvatData_varsetfile.txt.gz"))
varset <- getVarSet(varsetfile, unit = c("NEK1", "SOD1", "ABCA4"), varSetName = "High")
aggfile <- tempfile()
aggregate(x = gdb,
          varSet = varset,
          maxMAF = 0.001,
          output = aggfile,
          verbose = FALSE)

# connect to aggregateFile, see ?aggregateFile for more details
aggregatefile <- aggregateFile(aggfile)

# list units and samples in aggregatefile 
head(listUnits(aggregatefile))
#> [1] "ABCA4" "NEK1"  "SOD1" 
head(listSamples(aggregatefile))
#> [1] "ALS1" "ALS2" "ALS3" "ALS4" "ALS5" "ALS6"

# retrieve aggregates 
aggregates <- getUnit(aggregatefile, unit = "SOD1")

# see ?`assocTest-aggregateFile` for details on running association tests on an aggregateFile