simple_gadem: run the rGADEM suite

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

run the rGADEM suite

Description

This should provide a set of rGADEM results given an input file of sequences and a genome.

Usage

simple_gadem(
  inputfile,
  genome = "BSgenome.Hsapiens.UCSC.hs19",
  p = 0.1,
  e = 0,
  ...
)

Arguments

inputfile	Fasta or bed file containing sequences to search.
genome	BSgenome to read.
p	pvalue cutoff
e	evalue cutoff
...	Parameters for plotting the gadem result.

Value

A list containing slots for plots, the stdout output from gadem, the gadem result, set of occurences of motif, and the returned set of motifs.

See Also

[IRanges] [Biostrings] [rGADEM]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.