Create a new p4cProfile object. — p4cNewProfile • umi4cPackage

p4cNewProfile constructs a p4cProfile object from a genomic 2D track.

p4cNewProfile(
  track_nm,
  bait_chrom = gtrack.attr.get(track_nm[1], "Bait_chr"),
  bait_start = as.numeric(gtrack.attr.get(track_nm[1], "Bait_coord")),
  scope_5 = 250000,
  scope_3 = 250000,
  stat_type
)

Arguments

track_nm	2D genomic track name. Can also be a character vector of track names that will be pooled together by summation.
bait_chrom	Character. Bait chromosome.
bait_start	Integer. Start coordinate of the bait.
scope_5, scope_3	Define the scope of the profile. How many bases upstream and downstream of the bait should be used for generating the profile. Default is set to 250kb upstream and downstream.
stat_type	Define the method for calculating the profile contact intensities. Either "linear" or "log", for arithmetic or geometric means, respectively. Default is "linear".

Value

Returns a p4cProfile object.

Details

This function is the primary object constructor. It processes a 2D genomic track with (UMI)-4C raw contact data and returns a p4cProfile object.