annotate_intermut_dist_PID {YAPSA} | R Documentation

## Annotate the intermutation distance of variants per PID

### Description

The function annotates the intermutational distance to a PID wide data frame by applying `rainfallTransform` to every chromosome-specific subfraction of the PID wide data.

### Usage

    annotate_intermut_dist_PID(
      in_dat,
      in_CHROM.field = "CHROM",
      in_POS.field = "POS",
      in_mode = "min",
      in_verbose = FALSE
    )

### Arguments

`in_dat` | VRanges object or data frame which carries (at least) one column for the chromosome and one column for the position.
`in_CHROM.field` | String indicating which column of `in_dat` carries the chromosome information if dealing with data frames.
`in_POS.field` | String indicating which column of `in_dat` carries the position information if dealing with data frames.
`in_mode` | String passed to `rainfallTransform` indicating which method to choose for the computation of the intermutational distance.
`in_verbose` | Whether verbose or not.

### Value

VRanges object or data frame identical to `in_dat`, but with the intermutation distance annotated as an additional column on the right named `dist`.

### See Also

`annotate_intermut_dist_cohort`

`rainfallTransform`

### Examples

    test_df <- data.frame(
     CHROM=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5),
     POS=c(1,2,4,4,6,9,1,4,8,10,20,40,100,200),
     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"))
    min_dist_df <- annotate_intermut_dist_PID(test_df,in_CHROM.field="CHROM",
                                              in_POS.field="POS",
                                              in_mode="min")
    max_dist_df <- annotate_intermut_dist_PID(test_df,in_CHROM.field="CHROM",
                                              in_POS.field="POS",
                                              in_mode="max")
    min_dist_df
    max_dist_df

[Package YAPSA version 1.18.0 Index]