detect_onoffout: Detect local shape outliers based on a residual matrix

Description Usage Arguments

Description

This function identifies local shape variants by mining locally on/off abnormalities.

Usage

1
2
detect_onoffout(resmat, rawmat, exonset, winlength = 100,
  readconstr = 10, siglev = NULL, cutoff = NULL)

Arguments

resmat

a residual matrix from PCA, a data matrix subtracted by a low-rank matrix.

rawmat

a raw coverage matrix, dataI from process_data

exonset

exon/intron annotation matrix from annotate_pileup

winlength

the window size. Default is 100.

readconstr

the minimum reads count required to be considered for on/off local shape changes. Default is 10.


hyochoi/Scissors documentation built on July 3, 2019, 4:48 a.m.