VcfFilterRules-class: VcfFilterRules class objects
In kevinrue/TVTB: TVTB: The VCF Tool Box

Description Details Accessor methods Constructors Subsetting and Replacement Combining Evaluating Author(s) See Also Examples

The VcfFilterRules class can stores multiple types of filters applicable to various slots of VCF objects.

All arguments must be VcfFixedRules, VcfInfoRules, VcfVepRules, VcfFilterRules of FilterRules objects.

In the following code snippets x is a VcfFilterRules object.

active(x), active(x)<-: Get or set the active state of each filter rule in x. Inherited from FilterRules
vep(x), vep(x)<-: Gets or sets the INFO key where the Ensembl VEP predictions to use for filtering are stored.
type(x): Gets the type of each filter stored in a VcfFilterRules object. Read-only.

VcfFilterRules(...) constructs an VcfFilterRules object from VcfFixedRules, VcfInfoRules, VcfVepRules, and VcfFilterRules objects in ....

In the code snippets below, x is a VcfFilterRules object.

: x[i, drop = TRUE]: Subsets the filter rules using the same interface as for Vector. If all filter rules are of the same type and drop=TRUE (default), the resulting object is re-typed to the most specialised class, if possible. In other words, if all remaining filter rules are of type "vep", the object will be type as VcfVepRules.
: x[[i]]: Extracts an expression or function via the same interface as for List.
: x[i] <- value: Replaces a filter rule by one of any valid class (VcfFixedRules, VcfInfoRules, VcfVepRules, or VcfFilterRules). The active state(s), name(s), and type(s) (if applicable) are transferred from value.
: x[[i]] <- value: The same interface as for List. The default active state for new rules is TRUE.

In the following code snippets x is an object of class VcfFilterRules, while values and ... are objects from any of the classes VcfFixedRules, VcfInfoRules, VcfVepRules, or VcfFilterRules:

: append(x, values, after = length(x)): Appends the values onto x at the index given by after.
: c(x, ...,): Concatenates the filters objects in ... onto the end of x.

As described in the S4Vectors documentation:

eval(expr, envir, enclos) Evaluates each active rule in a VcfFilterRules instance (passed as the expr argument) in their respective context of a VCF object (passed as the envir argument).

evalSeparately(expr, envir, enclos):

subsetByFilter(x, filter)

summary(object)

See eval,FilterRules,ANY-method for details.

Kevin Rue-Albrecht

FilterRules, VcfFixedRules, VcfInfoRules, VcfVepRules, and VCF.

# Constructors ----

fixedR <- VcfFixedRules(list(
    pass = expression(FILTER == "PASS"),
    qual = expression(QUAL > 20)
    ))
fixedR

infoR <- VcfInfoRules(list(
    common = expression(MAF > 0.1), # minor allele frequency
    present = expression(ALT + HET > 0) # count of non-REF homozygotes
    ))
# ...is synonym to...
infoR <- VcfInfoRules(list(
    common = expression(MAF > 0.1), # minor allele frequency
    present = expression(ALT > 0 | HET > 0)
    ))
infoR

vepR <- VcfVepRules(list(
    missense = expression(Consequence %in% c("missense_variant")),
    CADD = expression(CADD_PHRED > 15)
    ))
vepR

vcfRules <- VcfFilterRules(fixedR, infoR, vepR)
vcfRules


# Accessors ----

## Type of each filter stored in the VcfFilterRules object
type(vcfRules)


# Example data ----

# VCF file
vcfFile <- system.file("extdata", "moderate.vcf", package = "TVTB")

# TVTB parameters
tparam <- TVTBparam(Genotypes("0|0", c("0|1", "1|0"), "1|1"))

# Pre-process variants
vcf <- VariantAnnotation::readVcf(vcfFile, param = tparam)
vcf <- VariantAnnotation::expand(vcf, row.names = TRUE)
vcf <- addOverallFrequencies(vcf, tparam)


# Applying filters to VCF objects ----

## Evaluate filters
eval(vcfRules, vcf)

## Evaluate filters separately
as.data.frame(evalSeparately(vcfRules, vcf))

# Interestingly, the only common missense variant has a lower CADD score
## Deactivate the CADD score filter
active(vcfRules)["CADD"] <- FALSE

## Subset VCF by filters (except CADD, deactivated above)
subsetByFilter(vcf, vcfRules)


# Subsetting and Replacement ----

v123 <- vcfRules[1:3]

# Extract the expression
v5expr <- vcfRules[[5]]
# Subset the object
v5obj <- vcfRules[5]

# Replace the expression (active reset to TRUE, original name retained)
v123[[2]] <- v5expr

# Replace the rule (active state and name transferred from v5obj)
v123[2] <- v5obj