centipede_data: Count readstarts at each nucleotide position in each BED...
In slowkow/CENTIPEDE.tutorial: A tutorial for running CENTIPEDE.

Description Usage Arguments Details Value

Count readstarts at each nucleotide position in each BED region.

1	centipede_data(bam_file, fimo_file, pvalue = 1e-04, flank_size = 100, ...)

`bam_file`	A BAM file with mapped DNase-Seq data.
`fimo_file`	A FIMO text file with PWM match sites.
`pvalue`	Select FIMO matches with p-value less than this.

The returend matrix "mat" has one row for each region in the BED file, and one column for each genomic position. The returned dataframe "regions" described each region with a p-value and q-value from FIMO.

A list with two items "mat" and "regions".

slowkow/CENTIPEDE.tutorial documentation built on May 30, 2019, 3:06 a.m.