submitGreatJob: Send requests to GREAT web server
In rGREAT: Client for GREAT Analysis

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

View source: R/great.R

Send requests to GREAT web server

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",
    help = TRUE)

`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.
`help`	Whether to print help messages.

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.

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

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.

Zuguang gu <z.gu@dkfz.de>

GreatJob-class

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)
}