gpatterns.adjust_read_pos: Change tidy_cpgs coordinates to fragments coordinates

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Change tidy_cpgs coordinates to fragments coordinates

Description

changes the coordinates of tidy_cpgs to the fragment coordinates. This is necessary to avoid over-counting of reads with coordinates that are shifted by several bps from the restriction site.

Usage

gpatterns.adjust_read_pos(
  calls,
  frag_intervs,
  maxdist = 0,
  rm_off_target = TRUE
)

Arguments

calls	tidy_cpgs data frame
frag_intervs	intervals set of the fragment
maxdist	maximal distance from fragments
rm_off_target	if TRUE - remove reads with distance > maxdist from frag_intervs if FALSE - those reads would be left unchanged

Value

tidy_cpgs data frame with chrom,start,end coordinates adjusted to fragment intervals

tanaylab/gpatterns documentation built on May 15, 2023, 6:23 p.m.