buildCNR: Build a CNR bundle (Copy Number, -Rounded)

In SingerLab/gac: Genetic Analysis of Cells

Build a CNR bundle (Copy Number, –Rounded)

Description

A CNR bundle is a 'list' composed of six matrices of class data.frame (mostly). The objective of the CNR is to keep single-cell data matrices syncronized and facilitate interaction with this data. The functions keepCells, excludeCells, addCells, subsetCNR, manipulate the complete bundle. Whereas addQC, addPheno, and addInfo, as the name implies they add columns to the QC, Y (phenotype), and chromInfo tables.

Usage

buildCNR(
  X,
  Y,
  qc,
  chromInfo,
  exprs = NULL,
  gene.index,
  bulk = FALSE,
  full.sync = TRUE,
  chromosome.order = c(1:22, "X", "Y", "MT"),
  ...
)

Arguments

X	bin or common segment copy number data. Can be in 'numeric' or integer form. By default it will be rounded by roundCNR.
Y	phenotype and additional cell-level annotation data nrow(Y) needs to equal ncol(X). There is no check for this yet. requires a 'cellID' column
qc	cell-level quality control metadata e.g. readcount, median bins, mapd, qc.status, or any other data that is technical about the cells. requires a 'cellID' column
chromInfo	bin chromosome and end position in base pairs. Needs to match X
exprs	slot for expression same-cell (same-sample) gene expression matrix. Must have cellID as rownames. default is NULL.
gene.index	a GRanges generated matrix to link bins to genes
bulk	logical specifying if data type is ratio from bulk DNA sequencing or integer copy number. If 'TRUE' data is an untransformed segment ratio. If 'FALSE' data is integer copy number
full.sync	sync cnr tables to preseve cell order, and sort chromInfo and gene.index based on chromsome and start position
chromosome.order	chromosome order. Default is a human genome primary assembly: 1:22, X, Y, and MT.
...	parameters passed to roundCNR

Value

A CNR bundle composed of genotype, phenotype, and metadata for a single-cell DNA copy number experiment. See 'getting_started.Rmd' vignette for additional details.

Examples

## Example Data
## Copy Number Matrix
data(copynumbers)

## phenotype data
data(pheno)

## Chromosome Information available in Baslan et al. 2012
data(chromInfo)

## gene index see getting started vignette
data(grch37.genes.5k)

cnr <- buildCNR(X = copynumbers, Y = pheno, qc = qc, exprs = NULL,
                chromInfo = chromInfo, gene.index = grch37.genes.5k)

class(cnr)

head(cnr$X[, 1:5])

head(cnr$Y[, 1:5])

head(cnr$genes[, 1:5])

## Not run: 
 saveRDS(cnr, file = "cnr.rds")

## End(Not run)

SingerLab/gac documentation built on March 29, 2025, 4:38 p.m.