annotate_intermut_dist_cohort {YAPSA} | R Documentation

## Annotate the intermutation distance of variants cohort-wide

### Description

The function annotates the intermutational distance to a cohort wide data frame by applying `annotate_intermut_dist_PID` to every PID-specific subfraction of the cohort wide data. Note that `annotate_intermut_dist_PID` calls `rainfallTransform`. If the PID information is missing, `annotate_intermut_dist_PID` is called directly for the whole input.

### Usage

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

### Arguments

`in_dat` | VRanges object, VRangesList, data frame or list of data frames which carries (at least) one column for the chromosome and one column for the position. Optionally, a column to specify the PID can be provided.
`in_CHROM.field` | String indicating which column of `in_df` carries the chromosome information
`in_POS.field` | String indicating which column of `in_df` carries the position information
`in_PID.field` | String indicating which column of `in_df` carries the PID information
`in_mode` | String passed through `annotate_intermut_dist_PID` to `rainfallTransform` indicating which method to choose for the computation of the intermutational distance.
`in_verbose` | Whether verbose or not.

### Value

VRanges object, VRangesList, data frame or list of data frames identical to `in_df` (reordered by `in_PID.field`), but with the intermutation distance annotated as an additional column on the right named `dist`.

### See Also

`annotate_intermut_dist_PID`

`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"),
                          PID=c(1,1,1,2,2,2,1,1,2,2,2,1,1,2))
    test_df <- test_df[order(test_df$PID,test_df$CHROM,test_df$POS),]
    min_dist_df <-
      annotate_intermut_dist_cohort(test_df,in_CHROM.field="CHROM",
                                    in_POS.field="POS", in_PID.field="PID",
                                    in_mode="min")
    max_dist_df <-
      annotate_intermut_dist_cohort(test_df,in_CHROM.field="CHROM",
                                    in_POS.field="POS", in_PID.field="PID",
                                    in_mode="max")
    min_dist_df
    max_dist_df

[Package YAPSA version 1.12.0 Index]