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

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

Send requests to GREAT web server

submitGreatJob(gr, bg = NULL,
    species               = "hg19",
    includeCuratedRegDoms = TRUE,
    bgChoice              = ifelse(is.null(bg), "wholeGenome", "data"),
    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 = 300,
    max_tries = 10,
    version = "default")

`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.
`species`	Species. "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.
`bgChoice`	How to define background. If it is set as `data`, `bg` should be set as well.
`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 "3.0.0", "2.0.2". Shorten version numbers can also be used, such as using "3" or "3.0" is same as "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://bejerano-test.stanford.edu/great/public/html/index.php )

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.

When bg is set, some pre-processing is applied before submitting to GREAT server for the reason that GREAT needs gr should be exactly subsets of bg, which means for any region in gr, there must be a region in bg which is exactly the same. Taking following example:

for gr:

1 2	chr1 200 300 chr1 250 400

for bg:

1
2
3

    chr1 100 250
    chr1 300 500
    chr1 400 600

They will be transformed as: for gr:

1 2	chr1 200 250 chr1 300 400

for bg:

    chr1 100 199
    chr1 200 250
    chr1 300 400
    chr1 401 600

Zuguang gu <z.gu@dkfz.de>

GreatJob-class

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

# more parameters can be set for the job
## Not run: 
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)

## End(Not run)