Class to manage interactions with an aggdb

The aggregate method saves genotype aggregates compressed in an aggdb file. The aggdb class manages connecting/interacting with these files and retrieving units of interest.

Build an aggdb

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

Connect to an aggdb

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

Getters

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

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

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

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

• listParams(x): Return a list of parameters used to generate the aggdb.

• metadata(x), getGdbId(x), getRvatVersion(x): various methods to retrieve metadata from the aggdb.

Association testing

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

Merging

Aggdbs can be merged using the mergeAggDbs method.

See also

aggregate

mergeAggDbs

aggdbList

assocTest-aggdb

Examples

library(rvatData)
gdb <- create_example_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 aggdb, see ?aggdb for more details
aggdb <- aggdb(aggfile)

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

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

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