Calculates all potential paired interactions from a BED file

Calculates all potential paired interactions from a BED file

calcBedpe(
  bed,
  res = 10000,
  x = 100,
  decreasing = TRUE,
  interactions = "interchromosomal"
)

Arguments

bed

data.frame in narrowpeak format

res

bin resolution for output BEDPE

x

integer top x numer of strongest or weakest peaks

decreasing

logical order by decreasing

interactions

string filter for interchromosomal or intrachromosomal interactions

Value

Returns a data.table of BEDPE interactions