rGREAT (version 1.4.2)

submitGreatJob: Send requests to GREAT web server

Description

Send requests to GREAT web server

Usage

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")

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.

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".

Value

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

Details

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):

[object Object],[object Object],[object Object]

See Also

GreatJob-class

Examples

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

# more parameters can be set for the job
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)