mergeConsBin.z: Merge abnormal consecutive bins

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Merge consecutive abnormal bins into one larger event. Two consecutive bins will be merged if the maximum (minimum) of their two Z-scores if significantly lower (higher) than what is observed from a null distribution. The null distribution is simulated by taking the maximum (minimum) values of two Normal values. The variance of the simulated Normal is given as a parameter of the function.

Usage

mergeConsBin.z(res.df, fdr.th = 0.05, sd.null = 1, nb.sim = 1e+06,
  stitch.dist = 10000)

Arguments

res.df	a data.frame with the Z-scores. Columns 'chr', 'start', 'end' and 'z' are required.
fdr.th	the False Discovery Rate threshold.
sd.null	the estimated standard deviation of the Z-score null distribution. Usually, computed during P-value estimation by 'fdrtool.quantile'.
nb.sim	the number of simulated Z-scores for the P-value computation.
stitch.dist	the stitching distance, i.e. the maximum distance at which two bins will be merged.

Value

a data.frame similar to the input 'res.df' but with an extra 'nb.bin.cons' column (the number of bin merged for each event).

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.