makeSummarizedExperimentFromDataFrame {SummarizedExperiment} | R Documentation

## Make a RangedSummarizedExperiment from a data.frame or DataFrame

### Description

`makeSummarizedExperimentFromDataFrame` uses `data.frame` or `DataFrame` column names to create a GRanges object for the `rowRanges` of the resulting SummarizedExperiment object. It requires that non-range data columns be coercible into a `numeric` `matrix` for the SummarizedExperiment constructor. All columns that are not part of the row ranges attribute are assumed to be experiment data; thus, keeping metadata columns will not be supported. Note that this function only returns SummarizedExperiment objects with a single assay.

If metadata columns are to be kept, one can first construct the row ranges attribute by using the makeGRangesFromDataFrame function and subsequently creating the SummarizedExperiment.

### Usage

    makeSummarizedExperimentFromDataFrame(df,
                                        ...,
                                        seqinfo = NULL,
                                        starts.in.df.are.0based = FALSE)

### Arguments

`df` | A data.frame or DataFrame object. If not, then the function first tries to turn `df` into a data frame with `as.data.frame(df)`.
`...` | Additional arguments passed on to makeGRangesFromDataFrame
`seqinfo` | Either `NULL`, or a Seqinfo object, or a character vector of seqlevels, or a named numeric vector of sequence lengths. When not `NULL`, it must be compatible with the genomic ranges in `df` i.e. it must include at least the sequence levels represented in `df`.
`starts.in.df.are.0based` | `TRUE` or `FALSE` (the default). If `TRUE`, then the start positions of the genomic ranges in `df` are considered to be 0-based and are converted to 1-based in the returned GRanges object. This feature is intended to make it more convenient to handle input that contains data obtained from resources using the "0-based start" convention. A notorious example of such resource is the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables).

### Value

A RangedSummarizedExperiment object with rowRanges and a single assay

### Author(s)

M. Ramos

### See Also

- makeGRangesFromDataFrame

### Examples

    ## ---------------------------------------------------------------------
    ## BASIC EXAMPLES
    ## ---------------------------------------------------------------------

    # Note that rownames of the data.frame are also rownames of the result
    df <- data.frame(chr="chr2", start = 11:15, end = 12:16,
                     strand = c("+", "-", "+", "*", "."), expr0 = 3:7,
                     expr1 = 8:12, expr2 = 12:16,
                     row.names = paste0("GENE", letters[5:1]))
    df

    exRSE <- makeSummarizedExperimentFromDataFrame(df)

    exRSE

    assay(exRSE)

    rowRanges(exRSE)

[Package SummarizedExperiment version 1.10.1 Index]