annotate_intermut_dist_PID: Annotate the intermutation distance of variants per PID

Description Usage Arguments Value See Also Examples

View source: R/basic_functions.R

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

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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

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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.