GenomicRanges: makeGRangesFromDataFrame – R documentation

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makeGRangesFromDataFrame

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

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)
}

GenomicRanges

Representation and manipulation of genomic intervals

v1.42.0

Artistic-2.0

Authors

P. Aboyoun, H. Pagès, and M. Lawrence

Initial release