Compare contacts intensities between two profiles — p4cIntervalsMean • umi4cPackage

Compare contact intensities at specific genomic intervals.

p4cIntervalsMean(
  p4c_obj,
  ref_p4c_obj,
  start,
  end,
  min_win_cov = 30,
  rawdata = FALSE,
  max_scope = 1e+06
)

Arguments

p4c_obj	A `p4cProfile` object.
ref_p4c_obj	The `p4cProfile` object one wishes to compare to.
start, end	Start and end coordinates of the genomic interval.
min_win_cov	Controls the smoothing as described in `plot.p4cProfile`.
rowdata	Return raw molecule counts instead of smoothed data.

Details

When a genomic region is suspected to be defferentialy contacting between two profiles, it is possible to compare these two profiles in the same intervals by deriving the normalized contact values in that region. This function facilitates this task. It returns a data.frame with the either the row molecule counts if rowdata = TRUE or normalized other wise. The smoothing is controlled by min_win_cov.

The p-value is calculated for the entire interval with a chi-square test. However, it assumes the interval is <1Mb from the bait. If the interval is >1Mb from the bait max_scope should be increased accordingly.