CreateCasperObject: CreateCasperObject

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

Description

Creation of a casper object.

Usage

CreateCasperObject(raw.data, annotation, control.sample.ids, cytoband,
  loh.name.mapping, cnv.scale, loh.scale, method, loh,
  project = "casperProject", sequencing.type, expr.cutoff = 4.5,
  display.progress = TRUE, log.transformed = TRUE,
  centered.threshold = 3, window.length = 50, length.iterations = 50,
  vis.bound = 2, noise.thr = 0.3, genomeVersion = "hg19", ...)

Arguments

raw.data	the matrix of genes (rows) vs. cells (columns) containing the raw counts
annotation	data.frame containing positions of each gene along each chromosome in the genome
control.sample.ids	vector containing the reference (normal) cell (sample) names
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
loh.name.mapping	contains the cell (sample) name and the matching baf signal sample name
cnv.scale	maximum expression scale
loh.scale	maximum baf scale
method	analysis type: itereative or fixed (default: iterative)
loh	The original baf signal
sequencing.type	sequencing.type sequencing type: bulk or single-cell
expr.cutoff	expression cutoff for lowly expressed genes
log.transformed	indicates if the data log2 transformed or not. (default:TRUE)
centered.threshold
window.length	window length used for median filtering (default: 50)
length.iterations	increase in window length at each scale iteration (default: 50)
vis.bound	threshold for control normalized data for better visualization (default: 2)
genomeVersion	genomeVersion: hg19 or hg38 (default: hg19)

Value

casper

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