cisbp: Conversion of the CIS-BP motif database to k-mer space.

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.