CHANGES in VERSION 2.9.1

- change NCBI api to v2.
- use `exp(phyper(..., log.p = TRUE))` to get rid of zero p-values. Thank @andvon
  for the code contribution.

---------------------------------------

CHANGES in VERSION 2.5.7

- use `try()` to wrap on `seqlevelsStyle()` to get rid of the errors

----------------------------------------

CHANGES in VERSION 2.5.2

- add `getGeneSetsFromOrgDb()`

------------------------------------------

CHANGES in VERSION 2.5.1

- support extending from the whole genes

------------------------------------------

CHANGES in VERSION 2.1.9

- add `getKEGGGenome()`

------------------------------------------

CHANGES in VERSION 2.1.8

- add `getGenomeDateFromNCBI()`

-------------------------------------------

CHANGES in VERSION 2.1.4

* online great: the names of input regions are kept.
* region coordinates (1-based or zero-based) are adjusted in `getRegionGeneAssociations()`.

-------------------------------------------

CHANGES in VERSION 1.99.7

* Calculation has been speeded up.

--------------------------------------------

CHANGES in VERSION 1.99.6

* set `getGeneSetsFromBioMart()` public

---------------------------------------------

CHANGES in VERSION 1.99.2

* by default exclude gap regions
* chr prefix in `gr` is removed when `biomart_dataset` is set.

-----------------------------------------------

CHANGES in VERSION 1.99.0

* add `great()` and related functions to support local GREAT.
* add `shinyReport()` to export results into a shiny application.

-----------------------------------------------

CHANGES in VERSION 1.21.1

* parseRegionGeneAssociationFile(): parsing also considers positions with no sign.

-----------------------------------------------

CHANGES in VERSION 1.19.1

* add 'tsv' option in `getEnrichmentTables()`

------------------------------------------------

CHANGES in VERSION 1.17.1

* assign to foreName and backName when querying GREAT
* use rmarkdown for vignette
* support GREAT version 4.0.4
* add startup messages

------------------------------------------------

CHANGES in VERSION 1.15.1

* `plotRegionGeneAssociationGraphs()`: fixe a bug of wrong value of `par(mfrow)`.
* fixed warnings of Rd files.

-------------------------------------------------

CHANGES in VERSION 1.13.3

* parse error message from GREAT

---------------------------------------------------

CHANGES in VERSION 1.13.1

* `plotRegionGeneAssociationGraphs()`: `par(mfrow)` is automatically set
  according to the length of `type`.

----------------------------------------------------

CHANGES in VERSION 1.11.1

* save regions in gzip file then submit to GREAT
* will not change the content of the input regions

----------------------------------------------------

CHANGES in VERSION 1.9.1

* change url according to changes on GREAT website

-----------------------------------------------------

CHANGES in VERSION 1.7.1

* submitGreatJob(): remove additional column by pintersect()

-----------------------------------------------------

CHANGES in VERSION 1.5.3

* if background is provided, input regions are automaticially adjusted
  to make sure all input regions are subset of backgrounds.

------------------------------------------------------

CHANGES in VERSION 1.3.3

* documentations were improved.
* test files are moved to tests/testthat

--------------------------------------------------------

CHANGES in VERSION 1.3.2

* bug fixed when background is self-provided.

--------------------------------------------------------

CHANGES in VERSION 1.3.1

* fixed a bug when gene symbol annotated by GREAT is ''
* print warnings when GREAT gives warnings

--------------------------------------------------------

CHANGES in VERSION 1.1.6

* versions of GREAT can be selected

--------------------------------------------------------

CHANGES in VERSION 1.1.5

* minor changes in documentations

---------------------------------------------------------

CHANGES in VERSION 1.1.4

* minor changes to adjust to github mirror

----------------------------------------------------------

CHANGES in VERSION 1.1.3

* error message is extract from GREAT now.
* default value of `bgChoice` depeneds on `gr` 

-----------------------------------------------------------

CHANGES in VERSION 1.1.2

* add dependency to base packages

-----------------------------------------------------------

CHANGES in VERSION 1.1.1

* enrivonment for the slots in `GreatJob` object are initialized
  inside `submitGreatJob`

-----------------------------------------------------------

CHANGES IN VERSION 0.99.5

* because analysis depends on internet connection, jump to 
  next version to enforce rebuilding of the vignette on bioconductor.

------------------------------------------------------------

CHANGES IN VERSION 0.99.4

* retrieve categories and corresponding ontologies from GREAT

------------------------------------------------------------
