Description Usage Arguments Details Value See Also
View source: R/find_motifs_genome.R
Calls findMotifsGenome.pl
to run motif analysis over a given
set of regions.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | find_motifs_genome(
x,
path,
genome,
motif_length = c(8, 10, 12),
scan_size = 100,
optimize_count = 8,
background = "automatic",
local_background = FALSE,
only_known = FALSE,
only_denovo = FALSE,
fdr_num = 0,
cores = parallel::detectCores(),
cache = .calc_free_mem()/4,
overwrite = FALSE,
keep_minimal = FALSE,
scale_logos = FALSE
)
|
x |
|
path |
where to write HOMER results |
genome |
ID of installed genome; check installed genomes using
|
motif_length |
vector of motif lengths to consider [default is
|
scan_size |
size of sequence to scan; this can be a numeric to
specify the number of bases to scan centered on the region, or
alternately can be set to "given" to scan the entire region;
if using "given", will use the "-chopify" option to cut large
background sequences to average of target sequence size
[default: |
optimize_count |
number of motifs to optimize [default: 8] |
background |
|
local_background |
a numeric scalar specifying number of equal size
regions around peaks to use as the local background
[by default this is not used, e.g. default: |
only_known |
turns off searching for denovo motifs |
only_denovo |
turns off searching for known motif enrichment |
fdr_num |
number of randomizations to perform to calculate FDR [default: 0] |
cores |
number of cores to use [default: all cores available] |
cache |
number in MB to use as cache to store sequences in memory [default: calculates free memory and divides by 4] |
overwrite |
overwrite an existing HOMER results directory
[default: |
keep_minimal |
remove all extra clutter from results, keep only
the essentials ( |
scale_logos |
whether to scale sequence logos by information content
[default: |
find_motifs_genome
runs the core HOMER motif enrichment function
from the R system, and in the process generates (as a side-effect)
a HOMER results directory.
This results directory is inspectable via a file browser, and contains a summary of the results as HTML files as well as text files.
For our purposes, within the directory two key files exist:
knownResults.txt
known motifs that are enriched
homerResults.all.motif
denovo motifs that are enriched
These two text files are the core results (all else can be discarded
by setting keep_minimal
to TRUE
, and are parsed downstream
by read_known_results
and read_denovo_results
.
Nothing; called for its side-effect of producing HOMER results
read_known_results
, read_denovo_results
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