findsmears: Generate the smear tables.
In ananjysong/SCclust: Single Cell Copy Number Analysis and Clustering

findsmears

R Documentation

Generate the smear tables.

Description

Given the breakpoint tables of all single cells generated by preprocess_segfile, extend the breakpoint bins into intervals containing several bins to allow for the uncertainty inherent in segmentation.

Usage

findsmears(breakpoint_table, smear = 2, keepboundaries = TRUE,
  mask_XY = TRUE)

Arguments

`breakpoint_table`	The breakpoint_table generated by `preprocess_segfile`.
`smear`	An integer. The number of spanning bins on one side. Default value: 2.
`keepboundaries`	Logical. If TRUE (Default), the bins on chromosome boundaries are kept.
`mask_XY`	Logical. If TRUE (Default), sex chromosomes (X, Y) are masked.

Value

smear_table. The cell names (profid), the chromosome (chrom) and bin location (bpstart, bpend) for the extended intervals with length of 2*smear and the change direction (bpsign).

ananjysong/SCclust documentation built on April 18, 2022, 10:06 p.m.