preprocess_segfile: Preprocess the segmented copy number profiles

In ananjysong/SCclust: Single Cell Copy Number Analysis and Clustering

Preprocess the segmented copy number profiles

Description

Input the segmented copy number profiles of some single cells, generate the breakpoint table which provides the genomic location and segmented copy number values for all cells.

Usage

preprocess_segfile(segfile, gc, eviltwins = NULL, ploidies = TRUE)

Arguments

segfile	The segmented copy number profiles of some single cells.
gc	The GC content table.
eviltwins	Bad cells. NULL or a vector of cell names.
ploidies	Logical. If TRUE (Default), the ploidies and homoloss information are taken into consideration.

Value

A list for two tables: breakpoint_table and ploidies_table. Each row in breakpoint_table correspond to one segment divided by breakpoints in one cell. The columns in breakpoint_table: cell names (profid), chromosome information(chrom, chromstart, chromend), absolute genomic location (abstart, absend), the bin location (segstarts, segends), count of bins in the segement (segbins) and the copy number value for the segment (segvals, cvals). Note: cvals are derived by incoporating ploidies.

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