run_homer: Perform HOMER Motif Enrichment Analysis using DE Genomic...

In stephenslab/fastTopics: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data

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 de_analysis.
k	Use the DE analysis results for this topic.
positions	A table of genomic positions corresponding to rows of the de_analysis results. Specifically, it should a data frame with four columns: “chr”, chromosome name or number; “start”, start position of genomic feature; “end”, end position of genomic feature; and “name”, the name of the genomic feature. If not specified, the genomic positions will be extracted from the row names of de$postmean, in which the row names are expected to be of the form chr_start_end. The genomic positions will be written to a BED file (see https://genome.ucsc.edu/FAQ/FAQformat.html for more information about BED files).
genome	The genome parameter passed to findMotifsGenome.pl.
subset	Describe input argument "subset" here.
homer.exec	The name or file path of the HOMER findMotifsGenome.pl excutable.
out.dir	The positions BED file and HOMER results are written to this directory.
homer.options	Character string used to override default findMotifsGenome.pl options.
verbose	When verbose = TRUE, progress information is printed to the console.

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.

stephenslab/fastTopics documentation built on March 29, 2025, 3:24 p.m.