Description Usage Arguments Details Value
Wrapper for running Seqgl.
1 2 3 4 | run.seqGL.wrapper(pos.regions, neg.regions, org = "hg19", res.dir,
dictionary.file, no.groups = 500, lambdas = c(0.01, 0.005, 0.001, 5e-04,
1e-04), no.cores = 1, motifs = FALSE, test.classes = c(1, -1),
fdr.cutoff = 0.05, ...)
|
pos.regions |
GRanges object of positive regions |
neg.regions |
GRanges object of negative regions. |
org |
Organism from which data was derived |
res.dir |
Output directory |
dictionary.file |
The positional wildcard dictionary file built using ChIPKernel |
no.groups |
Number of groups to use for group lasso |
lambdas |
Regularization parameters for cross validation |
no.cores |
Number of cores for parallel processing |
motifs |
Logical indicating if motifs should be computed |
test.classes |
Which of the test classes to find motifs for |
fdr.cutoff |
FDR cutoff for identifying examples best predicted by each group |
... |
Additional arguments to bulid.train.test.data |
The positive and negative regions will be split evenly to create training and test sets
GRanges object of enriched regions
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