annotate_intermut_dist_PID: Annotate the intermutation distance of variants per PID

In YAPSA: Yet Another Package for Signature Analysis

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

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