attribute_sequence_contex_indel: Attribution of sequence context and size for an INDEL

Description Usage Arguments Value Examples

View source: R/indel_functions.R

Description

The function is a wrapper and uses getSequenceContext to annotate the sequence context.

Usage

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attribute_sequence_contex_indel(
  in_dat,
  in_REF.field = "REF",
  in_ALT.field = "ALT",
  in_verbose = FALSE,
  in_offsetL = 10,
  in_offsetR = 50
)

Arguments

in_dat

VRanges object or data frame which carries one column for the reference base and one column for the variant base

in_REF.field

String indicating which column of in_dat carries the reference base if dealing with data frames

in_ALT.field

String indicating which column of in_dat carries the variant base if dealing with data frames

in_verbose

Verbose if in_verbose=1

in_offsetL

Number of nucleotides which should be annotated downstream of the variant. Per default 10 bps are annotated

in_offsetR

Number of nucleotides which should be annotated upstream of the catiant. Per default 50 bps are annotated

Value

VRanges object or data frame with the same number rows and additional columns containing the type of INDEL (Ins = insertion and Del = deletion), the annotated sequence context of the defined length, the absolute number of exchanged nucleotides and the nucleotide exchange between in_REF.field and in_ALT.field.

Examples

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data(GenomeOfNl_raw)
GenomeOfNl_context <- attribute_sequence_contex_indel(
                                   in_dat = head(GenomeOfNl_raw),
                                   in_REF.field = "REF",
                                   in_ALT.field = "ALT",
                                   in_verbose = FALSE,
                                   in_offsetL= 10, in_offsetR=50)
GenomeOfNl_context

slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.