makeGRangesFromDataFrame {GenomicRanges} | R Documentation

## Make a GRanges object from a data.frame or DataFrame

### Description

`makeGRangesFromDataFrame` takes a data-frame-like object as input and tries to automatically find the columns that describe genomic ranges. It returns them as a GRanges object.

`makeGRangesFromDataFrame` is also the workhorse behind the coercion method from data.frame (or DataFrame) to GRanges.

### Usage

    makeGRangesFromDataFrame(df,
                             keep.extra.columns=FALSE,
                             ignore.strand=FALSE,
                             seqinfo=NULL,
                             seqnames.field=c("seqnames", "seqname",
                                              "chromosome", "chrom",
                                              "chr", "chromosome_name",
                                              "seqid"),
                             start.field="start",
                             end.field=c("end", "stop"),
                             strand.field="strand",
                             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)`.
`keep.extra.columns` | `TRUE` or `FALSE` (the default). If `TRUE`, the columns in `df` that are not used to form the genomic ranges of the returned GRanges object are then returned as metadata columns on the object. Otherwise, they are ignored. If `df` has a `width` column, then it's always ignored.
`ignore.strand` | `TRUE` or `FALSE` (the default). If `TRUE`, then the strand of the returned GRanges object is set to `"*"`.
`seqinfo` | Either `NULL`, or a Seqinfo object, or a character vector of unique sequence names (a.k.a. seqlevels), or a named numeric vector of sequence lengths. When not `NULL`, `seqinfo` must be compatible with the genomic ranges in `df`, that is, it must have one entry for each unique sequence name represented in `df`. Note that it can have additional entries i.e. entries for seqlevels not represented in `df`.
`seqnames.field` | A character vector of recognized names for the column in `df` that contains the chromosome name (a.k.a. sequence name) associated with each genomic range. Only the first name in `seqnames.field` that is found in `colnames(df)` is used. If no one is found, then an error is raised.
`start.field` | A character vector of recognized names for the column in `df` that contains the start positions of the genomic ranges. Only the first name in `start.field` that is found in `colnames(df)` is used. If no one is found, then an error is raised.
`end.field` | A character vector of recognized names for the column in `df` that contains the end positions of the genomic ranges. Only the first name in `start.field` that is found in `colnames(df)` is used. If no one is found, then an error is raised.
`strand.field` | A character vector of recognized names for the column in `df` that contains the strand associated with each genomic range. Only the first name in `strand.field` that is found in `colnames(df)` is used. If no one is found or if `ignore.strand` is `TRUE`, then the strand of the returned GRanges object is set to `"*"`.
`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 GRanges object with one element per row in the input.

If the `seqinfo` argument was supplied, the returned object will have exactly the seqlevels specified in `seqinfo` and in the same order. Otherwise, the seqlevels are ordered according to the output of the `rankSeqlevels` function (except if `df` contains the seqnames in the form of a factor-Rle, in which case the levels of the factor-Rle become the seqlevels of the returned object and with no re-ordering).

If `df` has non-automatic row names (i.e. `rownames(df)` is not `NULL` and is not `seq_len(nrow(df))`), then they will be used to set names on the returned GRanges object.

### Note

Coercing data.frame or DataFrame `df` into a GRanges object (with `as(df, "GRanges")`), or calling `GRanges(df)`, are both equivalent to calling `makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)`.

### Author(s)

H. Pagès, based on a proposal by Kasper Daniel Hansen

### See Also

- GRanges objects.

- Seqinfo objects and the `rankSeqlevels` function in the GenomeInfoDb package.

- The `makeGRangesListFromFeatureFragments` function for making a GRangesList object from a list of fragmented features.

- The `getTable` function in the rtracklayer package for an R interface to the UCSC Table Browser.

- DataFrame objects in the S4Vectors package.

### Examples

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

    df <- data.frame(chr="chr1", start=11:15, end=12:16,
                     strand=c("+","-","+","*","."), score=1:5)
    df
    makeGRangesFromDataFrame(df)  # strand value "." is replaced with "*"

    ## The strand column is optional:
    df <- data.frame(chr="chr1", start=11:15, end=12:16, score=1:5)
    makeGRangesFromDataFrame(df)

    gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)
    gr2 <- as(df, "GRanges")  # equivalent to the above
    stopifnot(identical(gr, gr2))
    gr2 <- GRanges(df)        # equivalent to the above
    stopifnot(identical(gr, gr2))

    makeGRangesFromDataFrame(df, ignore.strand=TRUE)
    makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
                                 ignore.strand=TRUE)

    makeGRangesFromDataFrame(df, seqinfo=paste0("chr", 4:1))
    makeGRangesFromDataFrame(df, seqinfo=c(chrM=NA, chr1=500, chrX=100))
    makeGRangesFromDataFrame(df, seqinfo=Seqinfo(paste0("chr", 4:1)))

    ## ---------------------------------------------------------------------
    ## ABOUT AUTOMATIC DETECTION OF THE seqnames/start/end/strand COLUMNS
    ## ---------------------------------------------------------------------

    ## Automatic detection of the seqnames/start/end/strand columns is
    ## case insensitive:
    df <- data.frame(ChRoM="chr1", StarT=11:15, stoP=12:16,
                     STRAND=c("+","-","+","*","."), score=1:5)
    makeGRangesFromDataFrame(df)

    ## It also ignores a common prefix between the start and end columns:
    df <- data.frame(seqnames="chr1", tx_start=11:15, tx_end=12:16,
                     strand=c("+","-","+","*","."), score=1:5)
    makeGRangesFromDataFrame(df)

    ## The common prefix between the start and end columns is used to
    ## disambiguate between more than one seqnames column:
    df <- data.frame(chrom="chr1", tx_start=11:15, tx_end=12:16,
                     tx_chr="chr2", score=1:5)
    makeGRangesFromDataFrame(df)

    ## ---------------------------------------------------------------------
    ## 0-BASED VS 1-BASED START POSITIONS
    ## ---------------------------------------------------------------------

    if (require(rtracklayer)) {
      session <- browserSession()
      genome(session) <- "sacCer2"
      query <- ucscTableQuery(session, "Assembly")
      df <- getTable(query)
      head(df)

      ## A common pitfall is to forget that the UCSC Table Browser uses the
      ## "0-based start" convention:
      gr0 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
                                          start.field="chromStart",
                                          end.field="chromEnd")
      head(gr0)

      ## The start positions need to be converted into 1-based positions,
      ## to adhere to the convention used in Bioconductor:
      gr1 <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE,
                                          start.field="chromStart",
                                          end.field="chromEnd",
                                          starts.in.df.are.0based=TRUE)
      head(gr1)
    }

[Package GenomicRanges version 1.40.0 Index]