attribute_sequence_contex_indel: Attribution of sequence context and size for an INDEL

In YAPSA: Yet Another Package for Signature Analysis

Description

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

Usage

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

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

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.