makePerFeatureDF: Create a per-feature data.frame
In scuttle: Single-Cell RNA-Seq Analysis Utilities

Description Usage Arguments Details Value Author(s) See Also Examples

Create a per-feature data.frame (i.e., where each row represents a feature) from a SingleCellExperiment, most typically for creating custom ggplot2 plots.

makePerFeatureDF(
  x,
  cells = NULL,
  assay.type = "logcounts",
  use.rowdata = TRUE,
  check.names = FALSE,
  exprs_values = NULL,
  check_names = NULL
)

`x`	A SingleCellExperiment object. This is expected to have non-`NULL` row names.
`cells`	Character vector specifying the features for which to extract expression profiles across cells.
`assay.type`	String or integer scalar indicating the assay to use to obtain expression values. Must refer to a matrix-like object with integer or numeric values.
`use.rowdata`	Logical scalar indicating whether row metadata of `x` should be included. Alternatively, a character or integer vector specifying the row metadata fields to use.
`check.names`	Logical scalar indicating whether column names of the output should be made syntactically valid and unique.
`exprs_values, check_names`	Soft-deprecated equivalents to the arguments above.

This function enables us to conveniently create a per-feature data.frame from a SingleCellExperiment. Each row of the returned data.frame corresponds to a row in x, while each column of the data.frame corresponds to one aspect of the (meta)data in x.

Columns are provided in the following order:

Columns named according to the entries of cells represent the expression values across features for the specified cell in the assay.type assay.
Columns named according to the columns of rowData(x) represent the row metadata variables. This consists of all variables if use.rowdata=TRUE, no variables if use.rowdata=FALSE, and only the specified variables if use.rowdata is set to an integer or character vector.

By default, nothing is done to resolve syntactically invalid or duplicated column names. check_names=TRUE, this is resolved by passing the column names through make.names. Of course, as a result, some columns may not have the same names as the original fields in x.

A data.frame containing one field per aspect of data in x - see Details. Each row corresponds to a feature (i.e., row) of x.

Aaron Lun

makePerCellDF, for the cell-level equivalent.

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
rowData(example_sce)$Length <- runif(nrow(example_sce))

df <- makePerFeatureDF(example_sce, cells="Cell_001")
head(df)