JASPAR-package: The Package for R modules for JASPAR databases
In JASPAR: R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices.
Description
Details
Value
Author(s)
References
See Also
Examples
Description
R modules for JASPAR databases
Details
Package: JASPAR
Type: Package
License: GPL (>= 2)
This package contains:
modules and functions for
JASPAR data processing and visualization.
An overview of functions
Function
Description
make_template Make a template
that feeds into JASPAR databases
## To install from online repositories (e.g. CRAN)
install.packages(pkgs="JASPAR",
repos="http://cran.r-project.org")
## Sometimes the offical repository might not be up to
date,
## then you may install it from a downloaded
source file;
## please replace '<current-version>'
with actual version numbers:
install.packages(pkgs="JASPAR_<current-version>.tar.gz",
repos=NULL)
## Load the package and get a complete list of functions,
use
library(JASPAR)
ls("package:JASPAR")
## help documantation of the package
help(JASPAR) #
this page
Value
NULL
Author(s)
Xiaobei Zhao
Maintainer: Xiaobei Zhao xiaobei (at) binf.ku.dk
References
Zhao et al (2013), "JASPAR 2013: An extensively expanded
and updated open-access database of transcription factor
binding profiles." (In preparation)
See citation("JASPAR") for BibTeX entries for
LaTeX users.
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
require(JASPAR) # load JASPAR
help(JASPAR) # a help document of JASPAR
## data(package="JASPAR") # a list of datasets available in JASPAR (TBA)
ls("package:JASPAR") # a list of functions available in JASPAR
help(package="JASPAR") # help documentation on JASPAR
citation("JASPAR") # citation for publications
demo("JASPAR-demo") # run the demo
## view JASPAR Description
packageDescription("JASPAR")
## ## view JASPAR vignette (TBA)
## vignette("JASPAR-vignette",package="JASPAR")
Example output
Loading required package: gtools
JASPAR-package package:JASPAR R Documentation
_T_h_e _P_a_c_k_a_g_e _f_o_r _R _m_o_d_u_l_e_s _f_o_r _J_A_S_P_A_R _d_a_t_a_b_a_s_e_s
_D_e_s_c_r_i_p_t_i_o_n:
R modules for JASPAR databases
_D_e_t_a_i_l_s:
Package: JASPAR
Type: Package
License: GPL (>= 2)
This package contains:
modules and functions for JASPAR data processing and
visualization.
An overview of functions
Function Description
'make_template' Make a template
that feeds into JASPAR databases
## To install from online repositories (e.g. CRAN)
install.packages(pkgs="JASPAR", repos="http://cran.r-project.org")
## Sometimes the offical repository might not be up to date,
## then you may install it from a downloaded source file;
## please replace '<current-version>' with actual version numbers:
install.packages(pkgs="JASPAR_<current-version>.tar.gz",
repos=NULL)
## Load the package and get a complete list of functions, use
library(JASPAR)
ls("package:JASPAR")
## help documantation of the package
help(JASPAR) # this page
_V_a_l_u_e:
'NULL'
_A_u_t_h_o_r(_s):
Xiaobei Zhao
Maintainer: Xiaobei Zhao <email: xiaobei (at) binf.ku.dk>
_R_e_f_e_r_e_n_c_e_s:
Zhao et al (2013), "JASPAR 2013: An extensively expanded and
updated open-access database of transcription factor binding
profiles." (_In preparation_)
See 'citation("JASPAR")' for BibTeX entries for LaTeX users.
_S_e_e _A_l_s_o:
'make_template'
_E_x_a_m_p_l_e_s:
require(JASPAR) # load JASPAR
help(JASPAR) # a help document of JASPAR
## data(package="JASPAR") # a list of datasets available in JASPAR (TBA)
ls("package:JASPAR") # a list of functions available in JASPAR
help(package="JASPAR") # help documentation on JASPAR
citation("JASPAR") # citation for publications
demo("JASPAR-demo") # run the demo
## view JASPAR Description
packageDescription("JASPAR")
## ## view JASPAR vignette (TBA)
## vignette("JASPAR-vignette",package="JASPAR")
[1] "make_template"
Information on package 'JASPAR'
Description:
Package: JASPAR
Version: 0.0.1
Date: 2012-11-26
Title: R modules for JASPAR databases: a collection of
transcription factor DNA-binding preferences,
modeled as matrices.
Author: Xiaobei Zhao <xiaobei@binf.ku.dk>
Published:
Maintainer: Xiaobei Zhao <xiaobei@binf.ku.dk>
Description: R modules for JASPAR data processing and
visualization
Depends: R (>= 2.9.0), gtools
Suggests:
Enhances:
License: GPL (>= 2)
URL:
Repository: CRAN
Packaged: 2012-11-26 20:05:08 UTC; xiaobei
Type: Package
LazyLoad: yes
Collate: 'zzz.R' 'hello.R' 'JASPAR-package.R'
'JASPAR-internal.R' 'make_template.R'
Date/Publication: 2012-11-27 13:49:14
Built: R 3.4.1; x86_64-pc-linux-gnu; 2017-09-23 07:38:40
UTC; unix
Index:
JASPAR-package The Package for R modules for JASPAR databases
make_template Make a template that feeds into JASPAR
databases
To cite the JASPAR package in publications use:
Zhao et al (2013), JASPAR 2013: An extensively expanded and updated
open-access database of transcription factor binding profiles. (In
preparation)
A BibTeX entry for LaTeX users is
@Article{,
author = {Xiaobei Zhao and et al.},
title = {JASPAR 2013: An extensively expanded and updated open-access database of transcription factor binding profiles},
journal = {TBA},
year = {2013},
volume = {TBA},
pages = {TBA},
number = {TBA},
url = {TBA},
}
demo(JASPAR-demo)
---- ~~~~~~~~~~~
> require(JASPAR)
> example("make_template",package="JASPAR")
mk_tmp> x <-
mk_tmp+ rbind(
mk_tmp+ c(3, 0, 0, 0, 0, 0),
mk_tmp+ c(8, 0, 23, 0, 0, 0),
mk_tmp+ c(2, 23, 0, 23, 0, 24),
mk_tmp+ c(11, 1, 1, 1, 24, 0)
mk_tmp+ )
mk_tmp> PARAM <-
mk_tmp+ list(
mk_tmp+ INT_ID=NULL,
mk_tmp+ BASE_ID="MA0006",
mk_tmp+ COLLECTION="CORE",
mk_tmp+ VERSION=1,
mk_tmp+ NAME="Arnt-Ahr",
mk_tmp+ SPECIES="10090")
mk_tmp> TAG <-
mk_tmp+ list(
mk_tmp+ class="bHLH",
mk_tmp+ medline="7592839",
mk_tmp+ tax_group="vertebrate",
mk_tmp+ sysgroup="vertebrate",
mk_tmp+ acc="P30561",
mk_tmp+ acc="P53762",
mk_tmp+ comment="dimer",
mk_tmp+ type="SELEX",
mk_tmp+ newest=1
mk_tmp+ )
mk_tmp> cat(make_template(x=x,PARAM=PARAM,TAG=TAG))
`x' is a matrix without specific rownames, treating the rows as
in order of A, C, G, T.
BASE_ID MA0006
COLLECTION CORE
VERSION 1
NAME Arnt-Ahr
SPECIES 10090
TAG class bHLH
TAG acc P30561
TAG acc P53762
TAG medline 7592839
TAG tax_group vertebrate
TAG type SELEX
TAG newest 1
TAG comment dimer
TAG sysgroup vertebrate
A [ 3 0 0 0 0 0 ]
C [ 8 0 23 0 0 0 ]
G [ 2 23 0 23 0 24 ]
T [ 11 1 1 1 24 0 ]
//
Package: JASPAR
Version: 0.0.1
Date: 2012-11-26
Title: R modules for JASPAR databases: a collection of transcription
factor DNA-binding preferences, modeled as matrices.
Author: Xiaobei Zhao <xiaobei@binf.ku.dk>
Published:
Maintainer: Xiaobei Zhao <xiaobei@binf.ku.dk>
Description: R modules for JASPAR data processing and visualization
Depends: R (>= 2.9.0), gtools
Suggests:
Enhances:
License: GPL (>= 2)
URL:
Repository: CRAN
Packaged: 2012-11-26 20:05:08 UTC; xiaobei
Type: Package
LazyLoad: yes
Collate: 'zzz.R' 'hello.R' 'JASPAR-package.R' 'JASPAR-internal.R' .....
Date/Publication: 2012-11-27 13:49:14
Built: R 3.4.1; x86_64-pc-linux-gnu; 2017-09-23 07:38:40 UTC; unix
-- File: /usr/local/lib/R/site-library/JASPAR/Meta/package.rds
JASPAR documentation built on May 2, 2019, 6:24 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Details Value Author(s) References See Also Examples
Description
R modules for JASPAR databases
Details
| Package: | JASPAR |
| Type: | Package |
| License: | GPL (>= 2) |
This package contains:
modules and functions for
JASPAR data processing and visualization.
An overview of functions
| Function | Description |
make_template | Make a template that feeds into JASPAR databases |
## To install from online repositories (e.g. CRAN)
install.packages(pkgs="JASPAR",
repos="http://cran.r-project.org")
## Sometimes the offical repository might not be up to
date,
## then you may install it from a downloaded
source file;
## please replace '<current-version>'
with actual version numbers:
install.packages(pkgs="JASPAR_<current-version>.tar.gz",
repos=NULL)
## Load the package and get a complete list of functions,
use
library(JASPAR)
ls("package:JASPAR")
## help documantation of the package
help(JASPAR) #
this page
Value
NULL
Author(s)
Xiaobei Zhao
Maintainer: Xiaobei Zhao xiaobei (at) binf.ku.dk
References
Zhao et al (2013), "JASPAR 2013: An extensively expanded and updated open-access database of transcription factor binding profiles." (In preparation)
See citation("JASPAR") for BibTeX entries for
LaTeX users.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 | require(JASPAR) # load JASPAR
help(JASPAR) # a help document of JASPAR
## data(package="JASPAR") # a list of datasets available in JASPAR (TBA)
ls("package:JASPAR") # a list of functions available in JASPAR
help(package="JASPAR") # help documentation on JASPAR
citation("JASPAR") # citation for publications
demo("JASPAR-demo") # run the demo
## view JASPAR Description
packageDescription("JASPAR")
## ## view JASPAR vignette (TBA)
## vignette("JASPAR-vignette",package="JASPAR")
|
Example output
Loading required package: gtools
JASPAR-package package:JASPAR R Documentation
_T_h_e _P_a_c_k_a_g_e _f_o_r _R _m_o_d_u_l_e_s _f_o_r _J_A_S_P_A_R _d_a_t_a_b_a_s_e_s
_D_e_s_c_r_i_p_t_i_o_n:
R modules for JASPAR databases
_D_e_t_a_i_l_s:
Package: JASPAR
Type: Package
License: GPL (>= 2)
This package contains:
modules and functions for JASPAR data processing and
visualization.
An overview of functions
Function Description
'make_template' Make a template
that feeds into JASPAR databases
## To install from online repositories (e.g. CRAN)
install.packages(pkgs="JASPAR", repos="http://cran.r-project.org")
## Sometimes the offical repository might not be up to date,
## then you may install it from a downloaded source file;
## please replace '<current-version>' with actual version numbers:
install.packages(pkgs="JASPAR_<current-version>.tar.gz",
repos=NULL)
## Load the package and get a complete list of functions, use
library(JASPAR)
ls("package:JASPAR")
## help documantation of the package
help(JASPAR) # this page
_V_a_l_u_e:
'NULL'
_A_u_t_h_o_r(_s):
Xiaobei Zhao
Maintainer: Xiaobei Zhao <email: xiaobei (at) binf.ku.dk>
_R_e_f_e_r_e_n_c_e_s:
Zhao et al (2013), "JASPAR 2013: An extensively expanded and
updated open-access database of transcription factor binding
profiles." (_In preparation_)
See 'citation("JASPAR")' for BibTeX entries for LaTeX users.
_S_e_e _A_l_s_o:
'make_template'
_E_x_a_m_p_l_e_s:
require(JASPAR) # load JASPAR
help(JASPAR) # a help document of JASPAR
## data(package="JASPAR") # a list of datasets available in JASPAR (TBA)
ls("package:JASPAR") # a list of functions available in JASPAR
help(package="JASPAR") # help documentation on JASPAR
citation("JASPAR") # citation for publications
demo("JASPAR-demo") # run the demo
## view JASPAR Description
packageDescription("JASPAR")
## ## view JASPAR vignette (TBA)
## vignette("JASPAR-vignette",package="JASPAR")
[1] "make_template"
Information on package 'JASPAR'
Description:
Package: JASPAR
Version: 0.0.1
Date: 2012-11-26
Title: R modules for JASPAR databases: a collection of
transcription factor DNA-binding preferences,
modeled as matrices.
Author: Xiaobei Zhao <xiaobei@binf.ku.dk>
Published:
Maintainer: Xiaobei Zhao <xiaobei@binf.ku.dk>
Description: R modules for JASPAR data processing and
visualization
Depends: R (>= 2.9.0), gtools
Suggests:
Enhances:
License: GPL (>= 2)
URL:
Repository: CRAN
Packaged: 2012-11-26 20:05:08 UTC; xiaobei
Type: Package
LazyLoad: yes
Collate: 'zzz.R' 'hello.R' 'JASPAR-package.R'
'JASPAR-internal.R' 'make_template.R'
Date/Publication: 2012-11-27 13:49:14
Built: R 3.4.1; x86_64-pc-linux-gnu; 2017-09-23 07:38:40
UTC; unix
Index:
JASPAR-package The Package for R modules for JASPAR databases
make_template Make a template that feeds into JASPAR
databases
To cite the JASPAR package in publications use:
Zhao et al (2013), JASPAR 2013: An extensively expanded and updated
open-access database of transcription factor binding profiles. (In
preparation)
A BibTeX entry for LaTeX users is
@Article{,
author = {Xiaobei Zhao and et al.},
title = {JASPAR 2013: An extensively expanded and updated open-access database of transcription factor binding profiles},
journal = {TBA},
year = {2013},
volume = {TBA},
pages = {TBA},
number = {TBA},
url = {TBA},
}
demo(JASPAR-demo)
---- ~~~~~~~~~~~
> require(JASPAR)
> example("make_template",package="JASPAR")
mk_tmp> x <-
mk_tmp+ rbind(
mk_tmp+ c(3, 0, 0, 0, 0, 0),
mk_tmp+ c(8, 0, 23, 0, 0, 0),
mk_tmp+ c(2, 23, 0, 23, 0, 24),
mk_tmp+ c(11, 1, 1, 1, 24, 0)
mk_tmp+ )
mk_tmp> PARAM <-
mk_tmp+ list(
mk_tmp+ INT_ID=NULL,
mk_tmp+ BASE_ID="MA0006",
mk_tmp+ COLLECTION="CORE",
mk_tmp+ VERSION=1,
mk_tmp+ NAME="Arnt-Ahr",
mk_tmp+ SPECIES="10090")
mk_tmp> TAG <-
mk_tmp+ list(
mk_tmp+ class="bHLH",
mk_tmp+ medline="7592839",
mk_tmp+ tax_group="vertebrate",
mk_tmp+ sysgroup="vertebrate",
mk_tmp+ acc="P30561",
mk_tmp+ acc="P53762",
mk_tmp+ comment="dimer",
mk_tmp+ type="SELEX",
mk_tmp+ newest=1
mk_tmp+ )
mk_tmp> cat(make_template(x=x,PARAM=PARAM,TAG=TAG))
`x' is a matrix without specific rownames, treating the rows as
in order of A, C, G, T.
BASE_ID MA0006
COLLECTION CORE
VERSION 1
NAME Arnt-Ahr
SPECIES 10090
TAG class bHLH
TAG acc P30561
TAG acc P53762
TAG medline 7592839
TAG tax_group vertebrate
TAG type SELEX
TAG newest 1
TAG comment dimer
TAG sysgroup vertebrate
A [ 3 0 0 0 0 0 ]
C [ 8 0 23 0 0 0 ]
G [ 2 23 0 23 0 24 ]
T [ 11 1 1 1 24 0 ]
//
Package: JASPAR
Version: 0.0.1
Date: 2012-11-26
Title: R modules for JASPAR databases: a collection of transcription
factor DNA-binding preferences, modeled as matrices.
Author: Xiaobei Zhao <xiaobei@binf.ku.dk>
Published:
Maintainer: Xiaobei Zhao <xiaobei@binf.ku.dk>
Description: R modules for JASPAR data processing and visualization
Depends: R (>= 2.9.0), gtools
Suggests:
Enhances:
License: GPL (>= 2)
URL:
Repository: CRAN
Packaged: 2012-11-26 20:05:08 UTC; xiaobei
Type: Package
LazyLoad: yes
Collate: 'zzz.R' 'hello.R' 'JASPAR-package.R' 'JASPAR-internal.R' .....
Date/Publication: 2012-11-27 13:49:14
Built: R 3.4.1; x86_64-pc-linux-gnu; 2017-09-23 07:38:40 UTC; unix
-- File: /usr/local/lib/R/site-library/JASPAR/Meta/package.rds
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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