cisbp: Conversion of the CIS-BP motif database to k-mer space.
In Carldeboer/BrockmanR: K-mer-based analysis of chromatin state.
Description
Usage
Format
Details
Source
Description
A list containing: logical matrices of cognate (T) and non-cognate (F) k-mers for each human motif in CIS-BP (as defined in de Boer and Regev, 2017, bioRxiv);
information on how these matrices were created; information on the motifs themselves; information on the similarity between motifs.
Usage
1
Format
An object of class list of length 5.
Details
$binaryPWMScores a matrix of k-mers by motifs, where entry is True if k-mer is cognate of motif, and False otherwise; made from CIS-BP PWM motifs
$binaryPBMZScores a matrix of k-mers by motifs, where entry is True if k-mer is cognate of motif, and False otherwise; made from CIS-BP PBM Z-scores
$info a list of information describing how this was created.
$TFTable a data.frame with information about each motif (from CIS-BP: http://cisbp.ccbr.utoronto.ca/)
$similarMotifs a data.frame containing Motif_IDs and the Pearson r between the two (for those with r>0.5)
Source
http://cisbp.ccbr.utoronto.ca/
Carldeboer/BrockmanR documentation built on May 31, 2019, 2:19 p.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 Details Source
Description
A list containing: logical matrices of cognate (T) and non-cognate (F) k-mers for each human motif in CIS-BP (as defined in de Boer and Regev, 2017, bioRxiv); information on how these matrices were created; information on the motifs themselves; information on the similarity between motifs.
Usage
1 |
Format
An object of class list of length 5.
Details
$binaryPWMScores a matrix of k-mers by motifs, where entry is True if k-mer is cognate of motif, and False otherwise; made from CIS-BP PWM motifs $binaryPBMZScores a matrix of k-mers by motifs, where entry is True if k-mer is cognate of motif, and False otherwise; made from CIS-BP PBM Z-scores $info a list of information describing how this was created. $TFTable a data.frame with information about each motif (from CIS-BP: http://cisbp.ccbr.utoronto.ca/) $similarMotifs a data.frame containing Motif_IDs and the Pearson r between the two (for those with r>0.5)
Source
http://cisbp.ccbr.utoronto.ca/
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.