annotate_intermut_dist_cohort {YAPSA} | R Documentation |
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.
annotate_intermut_dist_cohort( in_dat, in_CHROM.field = "CHROM", in_POS.field = "POS", in_PID.field = NULL, in_mode = "min", in_verbose = FALSE )
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_POS.field |
String indicating which column of |
in_PID.field |
String indicating which column of |
in_mode |
String passed through |
in_verbose |
Whether verbose or not. |
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
.
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