annotate_intermut_dist_cohort: Annotate the intermutation distance of variants cohort-wide

In YAPSA: Yet Another Package for Signature Analysis

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

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