buildCNR | R Documentation |
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.
buildCNR(X, Y, qc, chromInfo, exprs = NULL, gene.index, bulk = FALSE, ...)
X |
bin or common segment copy number data. Can be in 'numeric'
or integer form. By default it will be rounded by |
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 |
... |
parameters passed to roundCNR |
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.
data(copynumbers) data(pheno) data(qc) data(chromInfo) data(gene.index) cnr <- buildCNR(X = copynumbers, Y = pheno, qc = qc, exprs = NULL, chromInfo = chromInfo, gene.index = gene.index) 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)
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