Package 'Rabe'

Assign variant IDs to a GRanges object based on overlap

Description

Assign variant IDs to a GRanges object based on overlap

Usage

assignToGRanges(variant_ids, targetGRanges, prune = TRUE)

Arguments

variant_ids	Character vector of variant IDs
targetGRanges	GenomicRanges::GRanges object
prune	Boolean, if TRUE will only rturn rows that overlap to >=1 variants

Details

This function considers strandedness when finding overlap. "A/G" variants will only be assigned to "+" stranded ranges, and vice versa. However, you must make sure that only "A/G" and "T/C" variants are included in the input.

Value

GenomicRanges::GRanges with an additional mcol $variant_ids. $variant_ids is a IRanges::CharacterList

Examples

vignette("rABE-analysis")

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Assign overlapping VCF variant IDs to a GRanges

Description

Assign overlapping VCF variant IDs to a GRanges

Usage

assignVariantIds(range, vcf, sep = ";")

Arguments

range	GenomicRanges::GRanges object
vcf	VariantAnnotation::VCF object
sep	Separator to use if >1 variants overlap to a range

Value

Input range except adding a $variant_ids column

Examples

vignette("rABE-analysis")

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Set difference of two variant tables

Description

Set difference of two variant tables

Usage

diffVariants(varTableX, varTableY)

Arguments

varTableX	variant table X
varTableY	variant table Y

Value

variant table of X \ Y (based on $variant_id)

Examples

vignette("rABE-analysis")

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Filter variants to include only Adenine base editing

Description

Filter variants to include only Adenine base editing

Usage

filterAdenineEditVariants(assignedRange, stranded = TRUE, pruning = TRUE)

Arguments

assignedRange	GenomicRanges::GRanges with $variant_ids column. You can assign variants with the function assignVariantIds().
stranded	Boolean whether to consider strandedness. If TRUE, A/G editing for '+' strand, T/C for '-' strand, raising error if any strand takes '*' value.
pruning	Whether to prune values in $variant_ids column. If TRUE, $variant_ids will only retain adenine base editing events. If FALSE, $variant_ids is not changed.

Value

GenomicRanges::GRanges containing ranges with at least one adenine base editing event.

Examples

vignette("rABE-analysis")

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Filter a single merged variant table

Description

Filter a single merged variant table

Usage

filterVariants(mergedVarTable, perc.limits, plot = TRUE)

Arguments

mergedVarTable	Single tibble::tibble of merged variants
perc.limits	Lower and upper limits of median mutation percentage.
plot	Boolean of whether to plot a simple histogram of mutation percentages

Value

Filtered merged variant table

Examples

vignette("rABE-analysis")

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Get 'confident' variants for downstream analysis

Description

Get 'confident' variants for downstream analysis

Usage

getConfidentVariantIds(variantTableList, print.stats = TRUE, min.occurence = 2)

Arguments

variantTableList	A list of variant tables. Each variant table must have $variant_id column.
print.stats	Boolean, whether to print statistics.
min.occurence	Integer, minimum number of occurences for a variant to be considered as 'confident'.

Value

A character vector of 'confident' variant IDs.

Examples

vignette("rABE-analysis")

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Convert GRanges with assigned variants into a tibble

Description

Convert GRanges with assigned variants into a tibble

Usage

getNameVarTable(assignedGRanges)

Arguments

assignedGRanges

an "assigned GRanges" (i.e., GenomicRanges::GRanges with names and variant_ids).

Value

A tibble::tibble with columns:

• name, character of name(assignedGRanges)

• variant_ids, list(character) of assignedGRanges$variant_ids

Examples

vignette("rABE-analysis")

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Get data frame of primary variants from a VCF file

Description

Get data frame of primary variants from a VCF file

Usage

getPrimaryVariantTable(vcf, variant_ids)

Arguments

vcf	VariantAnnotation::VCF object
variant_ids	Identifiers to subset the VCF object

Value

A data.frame of counts for primary variants of each ID queried.

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Return detailed variant information (mutation rate, counts for REF/ALT).

Description

Return detailed variant information (mutation rate, counts for REF/ALT).

Usage

getVariantTable(vcf, assignedRange)

Arguments

vcf	VariantAnnotation::VCF object
assignedRange	GenomicRanges::GRanges with $variant_ids column. You can assign variants with the function assignVariantIds().

Value

A tibble::tibble

Examples

vignette("rABE-analysis")

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Merge a list of variant tables into one table.

Description

Merge a list of variant tables into one table.

Usage

mergeVariants(variantTableList, variantIDsToKeep)

Arguments

variantTableList	list of variant tables.
variantIDsToKeep	which variant IDs to keep in the merged frame

Value

A single tibble::tibble of merged variant tables with following columns:

• variant_id, character vector

• variant_data list of tibble::tibble, each with columns $countREF, $countALT, $mutatin.perc.

Examples

vignette("rABE-analysis")

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Format summary of a numeric vector

Description

Format summary of a numeric vector

Usage

prettyFormatSummary(nums)

Arguments

nums	A numeric vector

Value

A character(1) showing standard summary statistics (i.e., 0/25/50/mean/75/100 quantiles).

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Prune a GenomicRanges containing variants to retain only A->G edits

Description

Prune a GenomicRanges containing variants to retain only A->G edits

Usage

pruneAdenineEditVariants(rangeWithVariants, stranded = TRUE)

Arguments

rangeWithVariants	GenomicRanges::GRanges with $variant_ids. Each range can contain multiple variant_ids separated by ⁠;⁠. Example $variant_ids = "chr2L:1_A/G;chr2L:100_C/A"
stranded	Boolean, whether to consider strand of the ranges

Value

GenomicRanges::GRanges with only A->G edits

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Convert A/G variant ID vector into GenomicRanges::GRanges

Description

Convert A/G variant ID vector into GenomicRanges::GRanges

Usage

variantID2GRanges(variant_ids)

Arguments

variant_ids

Character vector of VCF variant identifier. Example: "chr2L:1_A/G"

Details

Variant type is extracted but NOT checked at all. You must make sure that only "A/G" and "T/C" are present as input.

Value

GenomicRanges::GRanges object of the variants. All widths are one as this is record of single base mutations. The following mcols are defined:

• type, "A/G" (strand = "+") or "T/C" (strand = "-") to reflect variant type.

• variant_id, the original input as record

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