run.seqgl.wrapper: Wrapper for running Seqgl.

Description Usage Arguments Details Value

Description

Wrapper for running Seqgl.

Usage

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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, ...)

Arguments

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

Details

The positive and negative regions will be split evenly to create training and test sets

Value

GRanges object of enriched regions


ManuSetty/SeqGL documentation built on May 7, 2019, 2:46 p.m.