submitGreatJob: Send requests to GREAT web server

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/great.R

Description

Send requests to GREAT web server

Usage

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submitGreatJob(gr, bg = NULL,
    species               = "hg19",
    includeCuratedRegDoms = TRUE,
    rule                  = c("basalPlusExt", "twoClosest", "oneClosest"),
    adv_upstream          = 5.0,
    adv_downstream        = 1.0,
    adv_span              = 1000.0,
    adv_twoDistance       = 1000.0,
    adv_oneDistance       = 1000.0,
    request_interval = 60,
    max_tries = 10,
    version = DEFAULT_VERSION,
    base_url = "http://great.stanford.edu/public/cgi-bin")

Arguments

gr

A GRanges object or a data frame which contains at least three columns (chr, start and end). Regions for test.

bg

A GRanges object or a data frame. Background regions if needed. Note gr should be exactly subset of bg for all columns in gr. Check http://great.stanford.edu/help/display/GREAT/File+Formats#FileFormats-Whatshouldmybackgroundregionsfilecontain%3F for more explanation.

species

Species. "hg38", "hg19", "mm10", "mm9" are supported in GREAT version 4.x.x, "hg19", "mm10", "mm9", "danRer7" are supported in GREAT version 3.x.x and "hg19", "hg18", "mm9", "danRer7" are supported in GREAT version 2.x.x.

includeCuratedRegDoms

Whether to include curated regulatory domains.

rule

How to associate genomic regions to genes. See 'details' section.

adv_upstream

Unit: kb, only used when rule is basalPlusExt

adv_downstream

Unit: kb, only used when rule is basalPlusExt

adv_span

Unit: kb, only used when rule is basalPlusExt

adv_twoDistance

Unit: kb, only used when rule is twoClosest

adv_oneDistance

Unit: kb, only used when rule is oneClosest

request_interval

Time interval for two requests. Default is 300 seconds.

max_tries

Maximum times trying to connect to GREAT web server.

version

version of GREAT. The value should be "4.0.4", "3.0.0", "2.0.2". Shorten version numbers can also be used, such as using "4" or "4.0" is same as "4.0.4".

base_url

the url of cgi-bin path, only used when explicitly specified.

Details

Note: [On Aug 19 2019 GREAT released version 4](http://great.stanford.edu/help/display/GREAT/Version+History where it supports hg38 genome and removes some ontologies such pathways. submitGreatJob still takes hg19 as default. hg38 can be specified by the species = "hg38" argument. To use the older versions such as 3.0.0, specify as submitGreatJob(..., version = "3.0.0").

Note it is not the standard GREAT API. This function directly send data to GREAT web server by HTTP POST.

Following text is copied from GREAT web site ( http://great.stanford.edu/public/html/ )

Explanation of rule and settings with names started with 'adv_' (advanced settings):

basalPlusExt

Mode 'Basal plus extension'. Gene regulatory domain definition: Each gene is assigned a basal regulatory domain of a minimum distance upstream and downstream of the TSS (regardless of other nearby genes, controlled by adv_upstream and adv_downstream argument). The gene regulatory domain is extended in both directions to the nearest gene's basal domain but no more than the maximum extension in one direction (controlled by adv_span).

twoClosest

Mode 'Two nearest genes'. Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the nearest gene's TSS (controlled by adv_twoDistance) but no more than the maximum extension in one direction.

oneClosest

Mode 'Single nearest gene'. Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the midpoint between the gene's TSS and the nearest gene's TSS (controlled by adv_oneDistance) but no more than the maximum extension in one direction.

Value

A GreatJob-class class object which can be used to get results from GREAT server.

Note

takes hg19 as default. hg38 can be specified by the species = "hg38" argument. To use the older versions such as 3.0.0, specify as submitGreatJob(..., version = "3.0.0").**

Note it is not the standard GREAT API. This function directly send data to GREAT web server by HTTP POST.

Following text is copied from GREAT web site ( http://great.stanford.edu/public/html/ )

Explanation of rule and settings with names started with 'adv_' (advanced settings):

basalPlusExt

Mode 'Basal plus extension'. Gene regulatory domain definition: Each gene is assigned a basal regulatory domain of a minimum distance upstream and downstream of the TSS (regardless of other nearby genes, controlled by adv_upstream and adv_downstream argument). The gene regulatory domain is extended in both directions to the nearest gene's basal domain but no more than the maximum extension in one direction (controlled by adv_span).

twoClosest

Mode 'Two nearest genes'. Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the nearest gene's TSS (controlled by adv_twoDistance) but no more than the maximum extension in one direction.

oneClosest

Mode 'Single nearest gene'. Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the midpoint between the gene's TSS and the nearest gene's TSS (controlled by adv_oneDistance) but no more than the maximum extension in one direction.

Author(s)

Zuguang gu <z.gu@dkfz.de>

See Also

GreatJob-class

Examples

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set.seed(123)
bed = circlize::generateRandomBed(nr = 1000, nc = 0)
job = submitGreatJob(bed, version = "3.0.0")
job

# more parameters can be set for the job
if(FALSE) { # suppress running it when building the package
    # current GREAT version is 4.0.1
    job = submitGreatJob(bed, species = "mm9")
    job = submitGreatJob(bed, bg, species = "mm9", bgChoise = "data")
    job = submitGreatJob(bed, adv_upstream = 10, adv_downstream = 2, adv_span = 2000)
    job = submitGreatJob(bed, rule = "twoClosest", adv_twoDistance = 2000)
    job = submitGreatJob(bed, rule = "oneClosest", adv_oneDistance = 2000)
}

jokergoo/rGREAT documentation built on April 29, 2020, 6:24 p.m.