de novo Motif Discovery with STREME.

MotifDiscovery(
  peak.df = NULL,
  diff.peak = NULL,
  inte.res = NULL,
  peak.motif.key = NULL,
  genome,
  signif = "padj",
  signif.threshold = 0.05,
  l2fc.threshold = 0,
  peak.mode = c("consensus", "diff"),
  samtools.path = NULL,
  streme.path = NULL,
  streme.paras = "--nmotifs 50 --minw 8 --maxw 15 --thresh 0.05 --align center",
  out.folder = NULL,
  show.html = TRUE
)

Arguments

peak.df	Dataframe contains peaks, should contains chr, start, stop columns. Default: NULL.
diff.peak	Dataframe contains differential peaks, the rownames should be peak annotations results. Default: NULL.
inte.res	The Dataframe contains integrated results. `peak.df`, `diff.peak` and `inte.res` cannot be empty at the same time. Dafault: NULL.
peak.motif.key	The key type of integrated results ("Type" column of `inte.res`) or regulation type of differential peaks (Up_regulated, Not_regulated, Down_regulated) to perfrom de novo motif discovery. Used when `inte.res` is not NULL. Dafault: NULL.
genome	The genome fasta path.
signif	Significance criterion to get differential peaks. Used when `diff.peak` is not NULL. For DESeq2 results, can be chosen from padj, pvalue. For edgeR results, can be chosen from FDR, PValue. Default: padj.
signif.threshold	Significance threshold to get differential peaks. Used when `diff.peak` is not NULL. Default: 0.05.
l2fc.threshold	Log2 fold change threshold to get differential peaks. Used when `diff.peak` is not NULL. Default: 0.
peak.mode	The source of `inte.res` results, choose from consensus (consensus mode) and diff (differential analysis). Default: consensus.
samtools.path	The path to samtools (the version should >=1.9). Default: NULL (conduct automatic detection).
streme.path	The path to MEME's streme. Default: NULL (conduct automatic detection).
streme.paras	Parameter for MEME's streme. Default: "--nmotifs 50 --minw 8 --maxw 15 --thresh 0.05 --align center".
out.folder	Output folder. Default: NULL (current working directory).
show.html	Logical value, whether to show the results with pop-up window. Default: TRUE.

Value

NULL.

Examples

# library(DEbPeak)
# # de novo motif discovery with peak sets
# peak.file = system.file("extdata", "debchip_peaks.bed", package = "DEbPeak")
# peak.df = GetConsensusPeak(peak.file = peak.file)
# MotifDiscovery(peak.df = peak.df, genome = '/path/to/genome.fa',
#                streme.path = "/path/to/streme", samtools.path = "/path/to/samtools", out.folder = "/path/to/output")
# # de novo motif discovery with differential peaks
# MotifDiscovery(diff.peak = dds.peak.results.ordered, peak.motif.key = "Up_regulated",
#                genome = '/path/to/genome.fa', streme.path = "/path/to/streme",
#                samtools.path = "/path/to/samtools", out.folder = "/path/to/output")
# # de novo motif discovery with integrated results
# MotifDiscovery(inte.res = debatac.res, peak.motif.key = "Up_Up",
#                genome = '/path/to/genome.fa', peak.mode = "diff", streme.path = "/path/to/streme",
#                samtools.path = "/path/to/samtools", out.folder = "/path/to/output")