getChromInfoFromNCBI {GenomeInfoDb} | R Documentation

## Get chromosome information for an NCBI assembly

### Description

`getChromInfoFromNCBI` returns chromosome information like sequence names, lengths and circularity flags for a given NCBI assembly e.g. for GRCh38, ARS-UCD1.2, R64, etc...

Note that `getChromInfoFromNCBI` behaves slightly differently depending on whether the assembly is registered in the GenomeInfoDb package or not. See below for the details.

Use `registered_NCBI_assemblies` to list all the NCBI assemblies currently registered in the GenomeInfoDb package.

### Usage

    getChromInfoFromNCBI(assembly,
                         assembled.molecules.only=FALSE,
                         assembly.units=NULL,
                         recache=FALSE,
                         as.Seqinfo=FALSE)

    registered_NCBI_assemblies()

### Arguments

`assembly` | A single string specifying the name of an NCBI assembly (e.g. `"GRCh38"`). Alternatively, an assembly accession (GenBank or RefSeq) can be supplied (e.g. `"GCF_000001405.12"`).
`assembled.molecules.only` | If `FALSE` (the default) then chromosome information is returned for all the sequences in the assembly (unless `assembly.units` is specified, see below), that is, for all the chromosomes, plasmids, and scaffolds. If `TRUE` then chromosome information is returned only for the assembled molecules. These are the chromosomes (including the mitochondrial chromosome) and plasmids only. No scaffolds.
`assembly.units` | If `NULL` (the default) then chromosome information is returned for all the sequences in the assembly (unless `assembled.molecules.only` is set to `TRUE`, see above), that is, for all the chromosomes, plasmids, and scaffolds. `assembly.units` can be set to a character vector containing the names of Assembly Units (e.g. `"non-nuclear"`) in which case chromosome information is returned only for the sequences that belong to these Assembly Units.
`recache` | `getChromInfoFromNCBI` uses a cache mechanism so the chromosome information of a given assembly only gets downloaded once during the current R session (note that the caching is done in memory so cached information does NOT persist across sessions). Setting `recache` to `TRUE` forces a new download (and recaching) of the chromosome information for the specified assembly.
`as.Seqinfo` | `TRUE` or `FALSE` (the default). If `TRUE` then a Seqinfo object is returned instead of a data frame. Note that only the `SequenceName`, `SequenceLength`, and `circular` columns of the data frame are used to make the Seqinfo object. All the other columns are ignored (and lost).

### Details

registered vs unregistered NCBI assemblies:

- All NCBI assemblies can be looked up by assembly accession (GenBank or RefSeq) but only registered assemblies can also be looked up by assembly name.

- For registered assemblies, the returned circularity flags are guaranteed to be accurate. For unregistered assemblies, a heuristic is used to determine the circular sequences.

Please contact the maintainer of the GenomeInfoDb package to request registration of additional assemblies.

### Value

For `getChromInfoFromNCBI`: By default, a 10-column data frame with columns:

1. `SequenceName`: character.

2. `SequenceRole`: factor.

3. `AssignedMolecule`: factor.

4. `GenBankAccn`: character.

5. `Relationship`: factor.

6. `RefSeqAccn`: character.

7. `AssemblyUnit`: factor.

8. `SequenceLength`: integer. Note that this column **can** contain NAs! For example this is the case in assembly Amel_HAv3.1 where the length of sequence MT is missing or in assembly Release 5 where the length of sequence Un is missing.

9. `UCSCStyleName`: character.

10. `circular`: logical.

For `registered_NCBI_assemblies`: A data frame summarizing all the NCBI assemblies currently registered in the GenomeInfoDb package.

### Author(s)

H. Pagès

### See Also

- `getChromInfoFromUCSC` for getting chromosome information for a UCSC genome.

- `getChromInfoFromEnsembl` for getting chromosome information for an Ensembl species.

- Seqinfo objects.

### Examples

    ## Internet access required!

    getChromInfoFromNCBI("GRCh37")

    getChromInfoFromNCBI("GRCh37", as.Seqinfo=TRUE)

    getChromInfoFromNCBI("GRCh37", assembled.molecules.only=TRUE)

    getChromInfoFromNCBI("TAIR10.1")

    getChromInfoFromNCBI("TAIR10.1", assembly.units="non-nuclear")

    ## List of NCBI assemblies currently registered in the package:
    registered_NCBI_assemblies()

    ## The GRCh38.p12 assembly only adds "patch sequences" to the GRCh38
    ## assembly:
    GRCh38 <- getChromInfoFromNCBI("GRCh38")
    table(GRCh38$SequenceRole)
    GRCh38.p12 <- getChromInfoFromNCBI("GRCh38.p12")
    table(GRCh38.p12$SequenceRole)  # 140 patch sequences (70 fix + 70 novel)

    ## Sanity checks:
    idx <- match(GRCh38$SequenceName, GRCh38.p12$SequenceName)
    stopifnot(!anyNA(idx))
    tmp1 <- GRCh38.p12[idx, ]
    rownames(tmp1) <- NULL
    tmp2 <- GRCh38.p12[-idx, ]
    stopifnot(
      identical(tmp1[ , -(5:7)], GRCh38[ , -(5:7)]),
      identical(tmp2, GRCh38.p12[GRCh38.p12$AssemblyUnit == "PATCHES", ])
    )

[Package GenomeInfoDb version 1.28.4 Index]