attribute_nucleotide_exchanges {YAPSA} | R Documentation

## Attribute the nucleotide exchange for an SNV

### Description

SNVs are grouped into 6 different categories (12/2 as reverse complements are summed over). This function defines the attribution.

### Usage

    attribute_nucleotide_exchanges(
      in_dat,
      in_REF.field = "REF",
      in_ALT.field = "ALT",
      in_verbose = FALSE
    )

### 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` | Whether verbose or not.

### Value

A character vector with as many rows as there are in `in_dat` which can be annotated (i.e. appended) to the input data frame.

### Examples

    test_df <- data.frame(
     CHROM=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5),
     POS=c(1,2,3,4,5,6,1,2,3,4,5,6,7,8),
     REF=c("C","C","C","T","T","T","A","A","A","G","G","G","N","A"),
     ALT=c("A","G","T","A","C","G","C","G","T","A","C","T","A","N"))
    test_df$change <- attribute_nucleotide_exchanges(
     test_df,in_REF.field = "REF",in_ALT.field = "ALT")
    test_df

[Package YAPSA version 1.20.1 Index]