Package 'UCSC.utils' reference manual

Title:	Low-level utilities to retrieve data from the UCSC Genome Browser
Description:	A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.
Authors:	Hervé Pagès [aut, cre]
Maintainer:	Hervé Pagès <[email protected]>
License:	Artistic-2.0
Version:	1.3.0
Built:	2024-10-31 06:23:44 UTC
Source:	https://github.com/bioc/UCSC.utils

Fetch UCSC track data

Description

Fetch the track data for a given UCSC genome/track.

Usage

fetch_UCSC_track_data(genome, primary_table, api.url=UCSC.api.url())
fetch_UCSC_track_data(genome, primary_table, api.url=UCSC.api.url())

Arguments

`genome`	A single string specifying the name of a UCSC genome e.g. `"hs1"`, `"danRer11"`, or `"wuhCor1"`. See `?list_UCSC_genomes` for how to get the list of valid UCSC genome names.
`primary_table`	A single string specifying the name of the primary table associated with the track from which to fetch the data. See `?list_UCSC_tracks` for how to get the list of tracks and associated primary tables for a given UCSC genome.
`api.url`	The URL of the UCSC API. By default, the URL returned by `UCSC.api.url()` is used. Note that what `UCSC.api.url()` returns is controlled by a global option. See `?UCSC.api.url` for more information.

Value

A data frame.

Examples

gorGor6_gap_data <- fetch_UCSC_track_data("gorGor6", "gap")
head(gorGor6_gap_data)

## --- Comparison with UCSC_dbselect() ---

gorGor6_gap_data2 <- UCSC_dbselect("gorGor6", "gap")

## Easy sanity checks.
stopifnot(
  identical(dim(gorGor6_gap_data), dim(gorGor6_gap_data2)),
  identical(colnames(gorGor6_gap_data), colnames(gorGor6_gap_data2))
)

## But the two data frames are not identical:
identical(gorGor6_gap_data, gorGor6_gap_data2)  # FALSE!

## However, they have the same content. Ony reason they're not
## identical is because their rows are not in the same order.
## Let's reorder the rows in the two data frames by genomic location,
## that is, first by chromosome, then by chromStart, and finally
## by chromEnd:
sort_rows <- function(gap_data) {
  oo <- order(gap_data$chrom, gap_data$chromStart, gap_data$chromEnd)
  gap_data <- gap_data[oo, ]
  rownames(gap_data) <- NULL
  gap_data
}

gorGor6_gap_data <- sort_rows(gorGor6_gap_data)
gorGor6_gap_data2 <- sort_rows(gorGor6_gap_data2)

## Now the two data frames are identical:
stopifnot(identical(gorGor6_gap_data, gorGor6_gap_data2))
gorGor6_gap_data <- fetch_UCSC_track_data("gorGor6", "gap")
head(gorGor6_gap_data)

## --- Comparison with UCSC_dbselect() ---

gorGor6_gap_data2 <- UCSC_dbselect("gorGor6", "gap")

## Easy sanity checks.
stopifnot(
  identical(dim(gorGor6_gap_data), dim(gorGor6_gap_data2)),
  identical(colnames(gorGor6_gap_data), colnames(gorGor6_gap_data2))
)

## But the two data frames are not identical:
identical(gorGor6_gap_data, gorGor6_gap_data2)  # FALSE!

## However, they have the same content. Ony reason they're not
## identical is because their rows are not in the same order.
## Let's reorder the rows in the two data frames by genomic location,
## that is, first by chromosome, then by chromStart, and finally
## by chromEnd:
sort_rows <- function(gap_data) {
  oo <- order(gap_data$chrom, gap_data$chromStart, gap_data$chromEnd)
  gap_data <- gap_data[oo, ]
  rownames(gap_data) <- NULL
  gap_data
}

gorGor6_gap_data <- sort_rows(gorGor6_gap_data)
gorGor6_gap_data2 <- sort_rows(gorGor6_gap_data2)

## Now the two data frames are identical:
stopifnot(identical(gorGor6_gap_data, gorGor6_gap_data2))

List UCSC chromosome sizes

Description

Get the chromosome sizes of a given UCSC genome.

Usage

get_UCSC_chrom_sizes(genome, api.url=UCSC.api.url(), recache=FALSE)
get_UCSC_chrom_sizes(genome, api.url=UCSC.api.url(), recache=FALSE)

Arguments

`genome`	A single string specifying the name of a UCSC genome e.g. `"hs1"`, `"mm39"`, or `"sacCer3"`. See `?list_UCSC_genomes` for how to get the list of valid UCSC genome names.
`api.url`	The URL of the UCSC API. By default, the URL returned by `UCSC.api.url()` is used. Note that what `UCSC.api.url()` returns is controlled by a global option. See `?UCSC.api.url` for more information.
`recache`	`get_UCSC_chrom_sizes()` uses a cache mechanism so the information retrieved for a given genome 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 sizes for the specified genome.

Value

A named numeric vector. The names on the vector are the UCSC chromosomes/sequences. The vector values are the corresponding lengths.

Note that the vector is not sorted in any particular order. In particular there's not guarantee that the chromosomes will precede the scaffolds.

Examples

get_UCSC_chrom_sizes("ce2")

get_UCSC_chrom_sizes("hg38")
get_UCSC_chrom_sizes("ce2")

get_UCSC_chrom_sizes("hg38")

List UCSC genomes

Description

Get the list of UCSC genomes.

Usage

list_UCSC_genomes(organism=NA, api.url=UCSC.api.url(), recache=FALSE)

get_organism_for_UCSC_genome(genome, api.url=UCSC.api.url(), recache=FALSE)
list_UCSC_genomes(organism=NA, api.url=UCSC.api.url(), recache=FALSE)

get_organism_for_UCSC_genome(genome, api.url=UCSC.api.url(), recache=FALSE)

Arguments

`organism`	By default all UCSC genomes are returned (in a data frame). When `organism` is specified, `list_UCSC_genomes()` will only return the rows associated with the specified organism. `organism` must be supplied as a single string that will be used to perform a search (with `grep()`) on the `organism` and `common_name` columns of the data frame to return. The search is case-insensitive.
`api.url`	The URL of the UCSC API. By default, the URL returned by `UCSC.api.url()` is used. Note that what `UCSC.api.url()` returns is controlled by a global option. See `?UCSC.api.url` for more information.
`recache`	`list_UCSC_genomes()` uses a cache mechanism so the list of genomes 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 list of genomes. In the case of `get_organism_for_UCSC_genome()`, the supplied `recache` value is just passed down to the internal call to `list_UCSC_genomes()`.
`genome`	A character vector of valid UCSC genomes e.g. `"hg38"`, `"mm39"`, or `"sacCer3"`.

Value

For list_UCSC_genomes: A data frame with 1 row per genome and 5 columns: organism, genome, common_name, tax_id, description.

For get_organism_for_UCSC_genome: A named character of the same length as the input containing the scientific names of the organisms associated with the supplied UCSC genomes.

Examples

list_UCSC_genomes("human")

list_UCSC_genomes("pacos")

get_organism_for_UCSC_genome(c("ce11", "xenTro10", "mpxvRivers"))
list_UCSC_genomes("human")

list_UCSC_genomes("pacos")

get_organism_for_UCSC_genome(c("ce11", "xenTro10", "mpxvRivers"))

List UCSC tracks and associated primary tables

Description

Get the list of tracks and associated primary tables for a given UCSC genome.

Usage

list_UCSC_tracks(genome, group=NULL,
                 api.url=UCSC.api.url(), recache=FALSE)
list_UCSC_tracks(genome, group=NULL,
                 api.url=UCSC.api.url(), recache=FALSE)

Arguments

`genome`	A single string specifying the name of a UCSC genome e.g. `"hg38"`, `"mm39"`, or `"sacCer3"`. See `?list_UCSC_genomes` for how to get the list of valid UCSC genome names.
`group`	`NULL` or a single string specifying the group of tracks to return. By default, all tracks are returned. Passing `group=NA` is accepted and will return only rows associated with tracks that don't belong to any group.
`api.url`	The URL of the UCSC API. By default, the URL returned by `UCSC.api.url()` is used. Note that what `UCSC.api.url()` returns is controlled by a global option. See `?UCSC.api.url` for more information.
`recache`	`list_UCSC_tracks()` uses a cache mechanism so the information retrieved for a given genome 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 list of tracks for the specified genome.

Value

A data frame with 1 row per track and 5 columns: track, primary_table, type, group, composite_track.

Note that columns group and composite_track can contain NAs.

Examples

## List all tracks for ce2 genome:
list_UCSC_tracks("ce2")

## List tracks in the "rna" group only:
list_UCSC_tracks("ce2", group="rna")

## Note that some tracks don't belong to any group:
list_UCSC_tracks("hg38", group=NA)
## List all tracks for ce2 genome:
list_UCSC_tracks("ce2")

## List tracks in the "rna" group only:
list_UCSC_tracks("ce2", group="rna")

## Note that some tracks don't belong to any group:
list_UCSC_tracks("hg38", group=NA)

Conveniently retrieve data from the UCSC MariaDB server

Description

A convenience utility to retrieve data from the UCSC MariaDB server via simple SQL SELECT statements.

Requires the RMariaDB package!

Usage

UCSC_dbselect(dbname, from, columns=NULL, where=NULL, MoreSQL=NULL,
              host="genome-mysql.soe.ucsc.edu", port=3306)
UCSC_dbselect(dbname, from, columns=NULL, where=NULL, MoreSQL=NULL,
              host="genome-mysql.soe.ucsc.edu", port=3306)

Arguments

`dbname`	A single string specifying the name of the database to connect to. This is usually the name of a valid UCSC genome e.g. `"hg38"`, `"mm39"`, or `"sacCer3"`. See `?list_UCSC_genomes` for how to get the list of valid UCSC genome names.
`from`	A single string specifying the input data, that is, the `FROM` clause of the `SELECT` statement. This is typically the name of an SQL table, or a join-clause, or a sub-query.
`columns`	`NULL` (the default), or a character vector specifying the columns to return. By default all columns are returned.
`where`	`NULL` (the default), or a single string specifying the `WHERE` clause of the `SELECT` statement.
`MoreSQL`	`NULL` (the default), or a character vector containing additional SQL clauses e.g. `GROUP BY`, `ORDER BY`, and/or `LIMIT` clauses.
`host`	A single string specifying the name of the server's host
`port`	The TCP/IP port to use to connect to the server.

Details

UCSC_dbselect is an alternative to fetch_UCSC_track_data that is more efficient and gives the user more control on what data to retrieve exactly from the server.

However, the downside is that UCSC_dbselect does not work with all tracks! This is because, not all track data are stored in a database: some tracks are actually file-based (e.g. bigBed tracks). See below for an example.

Value

A data frame.

Examples

### Retrieve full "ncbiGene" table ("NCBI Genes" track) for eboVir3:
UCSC_dbselect("eboVir3", "ncbiGene")

### Retrieve subset of "sgpGene" table ("SGP Genes" track) for hg38:
UCSC_dbselect("hg38", "sgpGene", where="chrom='chrM'")

### Retrieve subset of "gap" table for gorGor6:
columns <- c("chrom", "chromStart", "chromEnd", "type")
where <- "chrom='chrX' AND type='contig'"
UCSC_dbselect("gorGor6", "gap", columns=columns, where=where)

### With a LEFT JOIN and a LIMIT clause:
from <- paste("ncbiRefSeq LEFT JOIN ncbiRefSeqLink",
              "ON ncbiRefSeq.name=ncbiRefSeqLink.id")
res <- UCSC_dbselect("sacCer3", from, MoreSQL="LIMIT 5")
dim(res)

## WARNING: UCSC_dbselect() does not work with all tracks!
## For example it does not work with bigBed tracks:
subset(list_UCSC_tracks("hg38", group="genes"), grepl("bigBed 9", type))
## Not run: 
UCSC_dbselect("hg38", "crisprAllTargets")  # table doesn't exist!

## End(Not run)
### Retrieve full "ncbiGene" table ("NCBI Genes" track) for eboVir3:
UCSC_dbselect("eboVir3", "ncbiGene")

### Retrieve subset of "sgpGene" table ("SGP Genes" track) for hg38:
UCSC_dbselect("hg38", "sgpGene", where="chrom='chrM'")

### Retrieve subset of "gap" table for gorGor6:
columns <- c("chrom", "chromStart", "chromEnd", "type")
where <- "chrom='chrX' AND type='contig'"
UCSC_dbselect("gorGor6", "gap", columns=columns, where=where)

### With a LEFT JOIN and a LIMIT clause:
from <- paste("ncbiRefSeq LEFT JOIN ncbiRefSeqLink",
              "ON ncbiRefSeq.name=ncbiRefSeqLink.id")
res <- UCSC_dbselect("sacCer3", from, MoreSQL="LIMIT 5")
dim(res)

## WARNING: UCSC_dbselect() does not work with all tracks!
## For example it does not work with bigBed tracks:
subset(list_UCSC_tracks("hg38", group="genes"), grepl("bigBed 9", type))
## Not run: 
UCSC_dbselect("hg38", "crisprAllTargets")  # table doesn't exist!

## End(Not run)

Get or set the default UCSC API URL

Description

Convenience helper for getting or setting global option UCSC.api.url.

Usage

UCSC.api.url(api.url=NULL)
UCSC.api.url(api.url=NULL)

Arguments

api.url

A single string containing the URL to the alternative UCSC API to use by default.

For convenience, api.url can also be one of the following aliases:

"primary": alias for "https://api.genome.ucsc.edu" (primary URL, US West Coast);
"": same as "primary";
"europe": alias for "https://genome-euro.ucsc.edu/cgi-bin/hubApi" (Europe mirror);
"asia": alias for "https://genome-asia.ucsc.edu/cgi-bin/hubApi" (Asia mirror).

Details

Various functions in the UCSC.utils package query the UCSC REST API. This is the case for example for list_UCSC_genomes, get_UCSC_chrom_sizes, list_UCSC_tracks and more.

Global option UCSC.api.url controls the UCSC API URL that these functions use y default. The option is set to "https://api.genome.ucsc.edu" (primary URL, US West Coast) at package startup.

UCSC.api.url() and UCSC.api.url(some_url) are provided as convenient ways of doing getOption("UCSC.api.url") and options(UCSC.api.url=some_url), respectively.

Value

When called with no argument, UCSC.api.url() returns getOption("UCSC.api.url").

When passed an URL, UCSC.api.url(some_url) returns the previous URL, that is, the UCSC API URL that was previously used by default. Note that the previous URL is returned invisibly.

Examples

UCSC.api.url()  # current default value of the UCSC API URL
get_UCSC_chrom_sizes("ce11", recache=TRUE)

## Temporarily use the mirror in Europe:
previous_url <- UCSC.api.url("europe")
UCSC.api.url()  # new default value of the UCSC API URL

get_UCSC_chrom_sizes("ce11", recache=TRUE)

## Restore previous default value:
UCSC.api.url(previous_url)
UCSC.api.url()
UCSC.api.url()  # current default value of the UCSC API URL
get_UCSC_chrom_sizes("ce11", recache=TRUE)

## Temporarily use the mirror in Europe:
previous_url <- UCSC.api.url("europe")
UCSC.api.url()  # new default value of the UCSC API URL

get_UCSC_chrom_sizes("ce11", recache=TRUE)

## Restore previous default value:
UCSC.api.url(previous_url)
UCSC.api.url()

Package 'UCSC.utils'

Help Index

Fetch UCSC track data

Description

Usage

Arguments

Value

See Also

Examples

List UCSC chromosome sizes

Description

Usage

Arguments

Value

See Also

Examples

List UCSC genomes

Description

Usage

Arguments

Value

See Also

Examples

List UCSC tracks and associated primary tables

Description

Usage

Arguments

Value

See Also

Examples

Conveniently retrieve data from the UCSC MariaDB server

Description

Usage

Arguments

Details

Value

See Also

Examples

Get or set the default UCSC API URL

Description

Usage

Arguments

Details

Value

See Also

Examples