casper: The CaSpER Class

In akdess/CaSpER: Identify large-scale CNV events from single cell or bulk RNA-Seq data

Description

The CaSpER Class The casper object is required for performing CNV analysis on single-cell and bulk RNA-Seq. It stores all information associated with the dataset, including data, smoothed data, baf values, annotations, scale specific segments, scale specific large scale events etc.

Slots

raw.data

raw project data

data

lowly expressed genes are filtered from the data

loh

original baf signal

median.filtered.data

median filtered expression signal

loh.median.filtered.data

median filtered baf signal

centered.data

gene expression levels are centered around the mid-point. For each gene, the mid-point of expression level is computed among all the cells (or samples in bulk RNA-seq), then the mid-point expression level is subtracted from the expression levels

center.smoothed.data

cell centric expression centering is performed. For each cell (or sample), we compute the mid-point of the expression level then we subtract the mid-point expression from the expression levels of all the genes for the corresponding cel

control.normalized

control normalization is performed by subtracting reference expression values from the tumor expression values.

control.normalized.visbound

control normalized data is thresholded in order to perform better visualization.

control.normalized.visbound.noiseRemoved

noise is removed from control normalized and thresholded data.

large.scale.cnv.events

large scale CNV events identified by CaSpER

segments

CNV segments identified by CaSpER

cytoband

cytoband information downloaded from UCSC hg19: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz hg38:http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz

annotation

positions of each gene along each chromosome in the genome

annotation.filt

lowly expressed genes are filtered from gene annotation data.frame

control.sample.ids

vector containing the reference (normal) cell (sample) names

project.name

project name

genomeVersion

genomeVersion: hg19 or hg38

hmmparam

initial hmm parameters estimated from data

plotorder

cell (sample) ordering for heatmap plots

vis.bound

threshold for control normalized data for better visualization

noise.thr

noise threshold for better visualization

loh.name.mapping

containing the cell (sample) name and the matching baf signal sample name

sequencing.type

sequencing type: bulk or single-cell

cnv.scale

maximum expression scale

loh.scale

maximum baf scale

loh.shift.thr

baf shift threshold estimated from baf signal using gaussian mixture models

window.length

window length used for median filtering

length.iterations

increase in window length at each scale iteration

akdess/CaSpER documentation built on April 8, 2021, 8:59 a.m.