CyData-subset {cydar} | R Documentation

## Subsetting and combining CyData

### Description

Methods to subset and combine objects of the CyData class.

### Usage

    ## S4 method for signature 'CyData,ANY,ANY'
    x[i, j, ..., drop=TRUE]
    ## S4 replacement method for signature 'CyData,ANY,ANY,CyData'
    x[i, j] <- value
    ## S4 method for signature 'CyData'
    subset(x, i, j)

    ## S4 method for signature 'CyData'
    rbind(..., deparse.level=1)
    ## S4 method for signature 'CyData'
    c(x, ..., recursive=FALSE)
    ## S4 method for signature 'CyData'
    cbind(..., deparse.level=1)

### Arguments

`x` | A CyData object.
`i, j` | A vector of subscripts, indicating the rows and columns to be subsetted for `i` and `j`, respectively. Rows correspond to cell-groups while columns correspond to samples.
`...` | For `cbind`, `...` contains CyData objects to be combined column-wise. For `rbind` and `c`, `...` contains CyData objects to be combined row-wise. For `c`, any objects are additional to that already specified in `x`. For other methods, this argument is ignored.
`drop` | A logical scalar, ignored.
`value` | A CyData object to replace the entries in the specified `i` and `j`.
`deparse.level, recursive` | Addition arguments, ignored.

### Details

Subsetting of CyData objects consider groups of cells (e.g., clusters, hyperspheres) as the rows, and samples as the columns. Only the rows of `intensities` are affected during row-wise subsetting. Marker and cell information in `markerData`, `cellData` and `cellIntensities` is not modified.

A similar principle applies when combining different CyData objects, i.e., rows are groups of cells and columns are samples. Values of `markerData` and `cellIntensities` should be identical in the objects to be combined. Furthermore, for `cbind`, values of `intensities` should also be identical. Note that `c` is a synonym for `rbind`.

When replacing entries with `[<-`, `markerData`, `cellData` and `cellIntensities` should be identical in `x` and `value`. Column replacement also requires `intensities` and `cellAssignments` to be the same. Simultaneous row and column replacement is not allowed as this will introduce inconsistencies into the sample ID annotation.

### Value

A CyData object with different rows or columns, depending on whether subsetting or merging was performed.

### Author(s)

Aaron Lun

### Examples

    example(CyData) # Mocking up an object.

    cyd[1:5,]
    cyd[,6:10]
    rbind(cyd, cyd)
    cbind(cyd, cyd)

[Package cydar version 1.4.0 Index]