Class that represents a set of variants and weights

An S4 class to manage an individual varSet record. Usually multiple varSets will be included in a varSetList or varSetFile object, which can be generated using the buildVarSet method.

Slots

unit

Unit name (such as the gene or transcript ID)

varSetName

Name of the variant set (such as 'LOF', 'moderate', 'CADD')

VAR_id

VAR_ids included in the varSet

w

weights included in the varSet

metadata

metadata

Getters

In the following code snippets, x is a varSet object.

  • listVars(x): Return a vector of all VAR_ids included in the varSet

  • listWeights(x): Return a vector of all weights in the varSet

Retrieve genotypes

A varSet object can be supplied to the varSet parameter in the getGT() method to load the variants included in the varSet.

Examples

library(rvatData)
varsetfile <- varSetFile(rvat_example("rvatData_varsetfile.txt.gz"))
varset <- getVarSet(varsetfile, unit = c("NEK1"), varSetName = "High")[[1]]

# list variants and weights included in the varSet
listVars(varset)
#>  [1] "1324" "1329" "1330" "1331" "1342" "1350" "1354" "1358" "1362" "1366"
#> [11] "1377" "1384" "1390" "1394" "1407" "1408" "1410" "1416" "1422" "1423"
#> [21] "1424" "1429" "1446" "1449" "1451" "1454" "1459" "1461" "1483" "1484"
#> [31] "1485" "1493" "1496"
listWeights(varset)
#>  [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

# note that usually you'll work with varSets in either a varSetList or 
# a varSetFile (see ?varSetList and ?varSetFile)