run_homer {fastTopics} | R Documentation |
Perform HOMER Motif Enrichment Analysis using DE Genomic Positions
Description
Run HOMER motif finding algorithm
(findMotifsGenome.pl
) to identify motifs enriched for
differentially expressed (DE) genomic positions. See
http://homer.ucsd.edu for more information.
Usage
run_homer(
de,
k,
positions,
genome = "hg19",
subset = function(postmean, lpval, lfsr, rank, quantile) lfsr < 0.05,
homer.exec = "findMotifsGenome.pl",
out.dir = tempdir(),
homer.options = "-len 8,10,12 -size 200 -mis 2 -S 25 -p 1 -h",
verbose = TRUE
)
Arguments
de |
An object of class “topic_model_de_analysis”,
usually the result of running |
k |
Use the DE analysis results for this topic. |
positions |
A table of genomic positions corresponding to rows
of the |
genome |
The genome parameter passed to
|
subset |
Describe input argument "subset" here. |
homer.exec |
The name or file path of the HOMER
|
out.dir |
The positions BED file and HOMER results are written to this directory. |
homer.options |
Character string used to override default
|
verbose |
When |
Value
A data frame containing the motif enrichment results. It
is created from the knownResults.txt
HOMER output.
References
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H. and Glass, C. K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell 38, 576-589.