Description Usage Arguments Details Value Note Author(s) See Also Examples
Send requests to GREAT web server
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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 |
bg |
A |
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 |
adv_downstream |
Unit: kb, only used when rule is |
adv_span |
Unit: kb, only used when rule is |
adv_twoDistance |
Unit: kb, only used when rule is |
adv_oneDistance |
Unit: kb, only used when rule is |
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 |
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):
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
).
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.
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):
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
).
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.
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>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
}
|
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