getOverlapStats: Statistics of overlaps between two segment sets.

In raim/segmenTools: Tools for Functional Genome Exploration

Statistics of overlaps between two segment sets.

Description

Statistics of overlaps between two segment sets.

Usage

getOverlapStats(
  ovl,
  ovlth = 0.8,
  minj = 0.8,
  minf = 0.2,
  hrng = c(0.8, 1.2),
  tnum = NA,
  qnum = NA,
  qid = NA,
  tid = NA
)

Arguments

ovl	overlap table from segmentAnnotate
ovlth	threshold fraction of overlap of target and query to be counted as 'good' hit
minj	the minimal Jaccard index above which the fraction is reported as JaccPrcnt
minf	fraction cutoff, the Jaccard index reported for this fraction of test sets is reported as JaccCutoff
hrng	lower and upper thresholds of the ratio CDF (query length/target length); the fraction of 'best' hits within this range will be reported as 'height'
tnum	number of targets in the original call, required for total CDF ('acdf')
qnum	number queries in the original call, just passed to results
qid	ID for the query set, just passed on to results and used in plot
tid	ID for the target set, just passed on to results and used in plot

raim/segmenTools documentation built on Sept. 9, 2024, 5:24 p.m.