Description Usage Arguments Details
SeqGL pipeline
1 2 3 4 5 | run.seqGL(peaks.file, out.dir, data.type, org, span = 150,
max.examples = ifelse(data.type == "ChIP", 5000, 40000), no.cores = 1,
no.groups = ifelse(data.type == "ChIP", 20, 100),
dictionary.file = system.file("extdata/wildcard_dict_kmer8_mismatches2_alpha5_consecutive_mis.Rdata",
package = "SeqGL"))
|
peaks.file |
Bed file containing the peaks. See Details. |
out.dir |
Path to the output directory |
data.type |
ChIP or DNase: indicating the experiment though which the peaks were derived |
org |
IUPAC organism code. hg19, hg18, mm10, mm9, mm8 are supported. Note that the corresponding BSGenome package has to be installed. |
span |
Width of the peaks used for analysis. Default is 150 |
no.cores |
Number of cores for parallel processing |
no.groups |
Number of groups to use for group lasso |
dictionary.file |
The positional wildcard dictionary file built using ChIPKernel. A dicionary will be built if it not specified. |
max.exmamples |
Maximum examples for training. Note that group membership will be determined for all examples |
SeqGL results will be available in out.dir
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.