run.seqgl.wrapper: Wrapper for running Seqgl.

In ManuSetty/SeqGL: Group lasso for Dnase/ChIP-seq data

Description

Wrapper for running Seqgl.

Usage

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 March 14, 2021, 3:18 a.m.