attribute_sequence_contex_indel {YAPSA} | R Documentation

## Attribution of sequence context and size for an INDEL

### 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

[Package YAPSA version 1.18.0 Index]