chromVARmotifs

The goal of chromVARmotifs is to make it easy to use several different motif collections in R, particularly for use with motifmatchr and chromVAR packages. Motifs are stored as PWMatrixList objects (object from TFBSTools package).

Installation

Installation is easiest using the devtools package. The function install_github will install the package.

devtools::install_github("GreenleafLab/chromVARmotifs")

The TFBSTools package from Bioconductor is the only direct dependency; the PWMatrixList object from that package is used to store the motifs.

Motif collections included:

data("human_pwms_v1") #curated collection of human motifs from cisBP database
data("mouse_pwms_v1") #curated collection of mouse motifs from cisBP database
data("human_pwms_v2") #filtered collection of human motifs from cisBP database
data("mouse_pwms_v2") #filtered collection of mouse motifs from cisBP database
data("homer_pwms") #motifs from HOMER
data("encode_pwms") #motifs from ENCODE

Version 2

The script used to make the “version 2” motifs (curated from the large master list for less redundancy) is shown below:

library(chromVARmotifs)
library(dplyr)
library(tidyr)
library(data.table)
data("human_pwms_v1")
data("mouse_pwms_v1")

sout <- sapply(strsplit(names(human_pwms_v1), split = "_"), function(s) c(s[3]))
human_pwms_v2 <- human_pwms_v1[match(unique(sout), sout)]

sout <- sapply(strsplit(names(mouse_pwms_v1), split = "_"), function(s) c(s[3]))
mouse_pwms_v2 <- mouse_pwms_v1[match(unique(sout), sout)]

save(human_pwms_v2, file = 'human_pwms_v2.rda')
save(mouse_pwms_v2,  file = 'mouse_pwms_v2.rda')

Conversion to PWM

Motifs originally in position frequency matrix form were converted to PWMs as follows:

1. Except for homer_pwms, a 0.008 pseudocount was added. Frequencies were then re-normalized to sum to 1.
2. Frequencies were divided by 0.25
3. Computed the log of the relative frequencies

Curation of cisBP motifs

We curated the motifs from the cisBP database to ensure each TF regulator was represented by at least one motif while reducing redundancy for the motifs linked to each TF>

Sources

encode_pwms are based on http://compbio.mit.edu/encode-motifs/ homer_pwms are based on http://homer.ucsd.edu/homer/custom.motifs human_pwms_v1 and mouse_pwms_v1 are based on http://cisbp.ccbr.utoronto.ca/