loadBed

The function reads BED formatted files. The BED file format defined by UCSC: http://genome.ucsc.edu/FAQ/FAQformat.
 First three columns ("chrom", "chromStart", "chromEnd") are mandatory. The file fields may be separated by tabs,
 spaces or commas. If the BED file contains a header, it will be ignored. If a genome mask dataframe is provided,
 only data intersected with the mask will be retained. Resulting data is ordered by "chromStart" columns.

Bioinformatics

genomics

Create, Plot and Compare Replication Timing Profiles. The method is described in Muller et al., (2014) <doi: 10.1093/nar/gkt878>.

Dzmitry Batrakou

Repliscope

Replication Timing Profiling using DNA Copy Number

loadBed function

<dl><dt>file</dt>
<dd>Path to the BED file (string, mandatory)</dd>
<dt>genome</dt>
<dd>A mask dataframe to exclude data from the BED file (dataframe, optional).
The genome dataframe must contain "chrom" column and may further contain "chromStart" and "chromEnd" columns in this
 order.</dd>
<dt>name</dt>
<dd>A string to replace the 'name' column of the loaded BED file with (string, optional).</dd></dl>

Arguments

Load a BED formatted file. — loadBed

<dl>

<dt>file</dt>
<dd>Path to the BED file (string, mandatory)</dd>


<dt>genome</dt>
<dd>A mask dataframe to exclude data from the BED file (dataframe, optional).
The genome dataframe must contain "chrom" column and may further contain "chromStart" and "chromEnd" columns in this
 order.</dd>


<dt>name</dt>
<dd>A string to replace the 'name' column of the loaded BED file with (string, optional).</dd>

</dl>

loadBed: Load a BED formatted file.

Description

Usage

Arguments

Examples