BumpyDataFrameMatrix {BumpyMatrix} | R Documentation

## The BumpyDataFrameMatrix class

### Description

The BumpyDataFrameMatrix provides a two-dimensional object where each entry is a DataFrame. This is useful for storing data that has a variable number of observations per sample/feature combination, e.g., for inclusion as another assay in a SummarizedExperiment object.

### Details

In the following code snippets, `x` is a BumpyDataFrameMatrix.

`commonColnames(x)` will return a character vector with the names of the available commonColnames. This can be modified with `commonColnames(x) <- value`.

`x[i, j, k, ..., .dropk=drop, drop=TRUE]` will subset the BumpyDataFrameMatrix:

- If `k` is not specified, this will either produce another BumpyDataFrameMatrix corresponding to the specified submatrix, or a CompressedSplitDataFrameList containing the entries of interest if `drop=TRUE`.

- If `k` is specified, it should contain the names or indices of the columns of the underlying DataFrame to retain. For multiple fields or with `.dropk=FALSE`, a new BumpyDataFrameMatrix is returned with the specified columns in the DataFrame.

- If `k` only specifies a single column and `.dropk=TRUE`, a BumpyMatrix (or CompressedList, if `drop=TRUE`) corresponding to the type of the field is returned.

`x[i, j, k, ...] <- value` will modify `x` by replacing the specified values with those in the BumpyMatrix `value` of the same dimensions. If `k` is not specified, `value` should be a BumpyDataFrameMatrix with the same fields as `x`. If `k` is specified, `value` should be a BumpyDataFrameMatrix with the specified fields. If `k` contains a single field, `value` can also be a BumpyAtomicMatrix containing the values to use in that field.

All methods described for the BumpyMatrix parent class are available.

### Author(s)

Aaron Lun

### Examples

    library(S4Vectors)
    df <- DataFrame(x=runif(100), y=runif(100))
    f <- factor(sample(letters[1:20], nrow(df), replace=TRUE), letters[1:20])
    out <- split(df, f)

    # Making our BumpyDataFrameMatrix.
    mat <- BumpyMatrix(out, c(5, 4))
    mat[,1]
    mat[1,]

    # Subsetting capabilities.
    xmat <- mat[,,"x"]
    ymat <- mat[,,"y"]
    filtered <- mat[xmat > 0.5 & ymat > 0.5]
    filtered[,1]

    # Subset replacement works as expected.
    mat2 <- mat
    mat2[,,"x"] <- mat2[,,"x"] * 2
    mat2[,1]

[Package BumpyMatrix version 1.2.0 Index]