cen: A dataset ready to use with CENTIPEDE.

Description Usage Format

Description

A dataset ready to use with CENTIPEDE.

Usage

1

Format

A list with two items:

mat

A numeric matrix with counts of read start sites. Each row corresponds to a genomic site flanked by 100 bp. A single row contains information about the positive strand and the negative strand. So, for example, this dataset uses a transcription factor motif of length 13 bp and flanks of length 100 bp. Therefore, the matrix has 2 * (100 + 13 + 100) = 426 columns.

regions

A dataframe. Each row corresponds to a genomic site, in the same order as the matrix of counts. This has information from a run of FIMO using the 13 bp motif for STAT4.


slowkow/CENTIPEDE.tutorial documentation built on March 20, 2018, 3:23 p.m.