tf_equallength: The list contains an information taken from RegulonDB 8.2...
In RedJane/tfbs.qsam: The analysis of TFBS by QSAM
Description
Usage
Format
Source
See Also
Examples
Description
Very often RegulonDB contains entries for one TF with different binding site lengths. It might cause difficulties for TFBS analysis. To avoid the problem we created this list, all entries in it provide sequences with equal (most frequent) lengths.
Usage
1
Format
The format is:
List of 8
$ ArcA:List of 104
..$ :List of 11
.. ..$ EC : chr "ECK120011345"
.. ..$ pos : num [1:2] 41981 41995
.. ..$ strand : chr "reverse"
.. ..$ seq : chr "tatattaaatGTTAACAAAAATAAAacaaacggga"
.. ..$ effect : chr "+"
.. ..$ promoter: chr "caiTp"
.. ..$ from_tss: num 50
.. ..$ evidence: chr "[GEA|W|Gene expression analysis],[AIBSCS|W|Automated inference based on similarity to consensus sequences]"
.. ..$ length : int 15
.. ..$ mpot : num [1:121] -0.0613 -0.0612 -0.0611 -0.0611 -0.0611 ...
.. ..$ weight : num -6.2
.. [list output truncated]
Source
http://regulondb.ccg.unam.mx/menu/download/datasets/files/BindingSiteSet.txt
See Also
Examples
1
2
data(tf_equallength)
## maybe str(tf_equallength) ; plot(tf_equallength) ...
RedJane/tfbs.qsam documentation built on May 9, 2019, 9:37 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 Usage Format Source See Also Examples
Description
Very often RegulonDB contains entries for one TF with different binding site lengths. It might cause difficulties for TFBS analysis. To avoid the problem we created this list, all entries in it provide sequences with equal (most frequent) lengths.
Usage
1 |
Format
The format is: List of 8 $ ArcA:List of 104 ..$ :List of 11 .. ..$ EC : chr "ECK120011345" .. ..$ pos : num [1:2] 41981 41995 .. ..$ strand : chr "reverse" .. ..$ seq : chr "tatattaaatGTTAACAAAAATAAAacaaacggga" .. ..$ effect : chr "+" .. ..$ promoter: chr "caiTp" .. ..$ from_tss: num 50 .. ..$ evidence: chr "[GEA|W|Gene expression analysis],[AIBSCS|W|Automated inference based on similarity to consensus sequences]" .. ..$ length : int 15 .. ..$ mpot : num [1:121] -0.0613 -0.0612 -0.0611 -0.0611 -0.0611 ... .. ..$ weight : num -6.2 .. [list output truncated]
Source
http://regulondb.ccg.unam.mx/menu/download/datasets/files/BindingSiteSet.txt
See Also
Examples
1 2 | data(tf_equallength)
## maybe str(tf_equallength) ; plot(tf_equallength) ...
|
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.