varSetFile.RdAn S4 class to manage interactions with varSetFiles. varSets can be generated from annotations using
the buildVarSet() method. Specific units and/or annotations can be loaded using
the getVarSet method. A varSetFile can be used as input in assocTest() to perform
burden/single variant association tests on the varSets included in the varSetFile.
buildVarSet(x, ...): Generate a varSetList or varSetFile() that stores weighted variant sets
for use in association testing. This can be based on 1) annotations uploaded to the gdb or 2) a data.frame including annotations.
See buildVarSet() for details.
varSetFile(path, memlimit = 5000): Connect to a varSetFile object.
In the following code snippets, x is a varSetFile object.
getVarSet(x, unit, varSetName): Retrieve varSets for specified units and/or varSetNames.
Output will be of class varSetList.
listUnits(x): Return a vector of all units included in the varSetFile
listVarSets(x): Return a vector of all varSetNames included in the varSetFile
A varSetFile can be directly supplied to the assocTest() gdb method, using the
varSet parameter. Association tests will then be performed for each varSet included
in the varSetFile.
library(rvatData)
# Build a varSetFile including variants with a moderate predicted impact
gdb <- create_example_gdb()
varsetfile_moderate <- tempfile()
buildVarSet(object = gdb,
output = varsetfile_moderate,
varSetName = "Moderate",
unitTable = "varInfo",
unitName = "gene_name",
where = "ModerateImpact = 1")
#> Generated varSetFile: /var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825cdb4b7f7
#> varSetFile object
#> Path:/var/folders/cl/wvc0rvjx4vd5rzt2_fhpmfth0000gp/T//RtmpRC6myU/file1825cdb4b7f7
#> Units:12
# connect to the varSetFile
varsetfile <- varSetFile(varsetfile_moderate)
# list included units and varSets
units <- listUnits(varsetfile)
head(units)
#> [1] "ABCA4" "CYP19A1" "FUS" "IL3RA" "NEK1" "OPTN"
varsets <- listVarSets(varsetfile)
head(varsets)
#> [1] "Moderate" "Moderate" "Moderate" "Moderate" "Moderate" "Moderate"
# basic operations
length(varsetfile)
#> [1] 12
# metadata
metadata(varsetfile)
#> $rvatVersion
#> [1] "0.3.2"
#>
#> $gdbId
#> [1] "vmo8w57mh9lhjhijqf5ja9fu0suj"
#>
#> $genomeBuild
#> [1] "GRCh38"
#>
#> $creationDate
#> [1] "2025-02-12 12:29:26"
#>
getRvatVersion(varsetfile)
#> [1] "0.3.2"
getGdbId(varsetfile)
#> [1] "vmo8w57mh9lhjhijqf5ja9fu0suj"
# retrieve varSets
varsets <- getVarSet(varsetfile, unit = c("SOD1", "FUS"))
# this returns a varSetList, which is an in-memory representation of varSets
# most of the methods that work on a varSetFile also work on a varSetList (see ?varSetLit for details)
getVarSet(varsets, unit = "SOD1")
#> varSetList
#> Contains 1 records
#> [[1]]
#> unit=SOD1
#> varSetName=Moderate
#> VAR_id=1268,1270,1271,1273,1275,1276,1277,1278,1279,1281,1282,1283,1284,1285,1287,1288,1289,1290,1291,1292,1293,1294,1296,1297,1298,1299,1300,1304,1305,1306,1307,1308,1309,1312,1313,1314,1315,1316
#> w=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
#>
# see e.g., ?assocTest and ?aggregate for downstream methods that can loop through varsetfiles and varsetlists.