filtered

lymphoid_chr20_paired_filtered


<code>filtered</code> is a GenomicRangesList example object used as an example for the binomialHiC package. This GenomicRangesList contains reads from a human lymphoblastoid cell line HiC experiment (Lieberman-Aiden et al. 2009) for chr20, that were mapped to the genome, paired and PCR duplicate-filtered. 


datasets

This is a Hi-C analysis package using a cumulative
binomial test to detect interactions between distal genomic
loci that have significantly more reads than expected by chance
in Hi-C experiments. It takes mapped paired NGS reads as input
and gives back the list of significant interactions for a given
bin size in the genome.

Borbala Mifsud

GOTHiC

Binomial test for Hi-C data analysis

filtered function

The format is:
GenomicRangesList with 2 slots:
$paired_reads_1 contains the coordinates for one end of the paired reads
$paired_reads_2 contains the coordinates for the other end of the paired reads

Format

<code>filtered</code> is a GenomicRangesList example object used as an example for the binomialHiC package. This GenomicRangesList contains reads from a human lymphoblastoid cell line HiC experiment (Lieberman-Aiden et al. 2009) for chr20, that were mapped to the genome, paired and PCR duplicate-filtered.

filtered: A GenomicRangesList object used as an example in the GOTHiC package

Description

Usage

Arguments

Format

See Also

Examples