TSS.zebrafish.Zv9


TSS annotation for Danio rerio (Zv9) obtained from biomaRt


datasets

The package includes functions to retrieve the sequences
around the peak, obtain enriched Gene Ontology (GO) terms, find
the nearest gene, exon, miRNA or custom features such as most
conserved elements and other transcription factor binding sites
supplied by users. Starting 2.0.5, new functions have been
added for finding the peaks with bi-directional promoters with
summary statistics (peaksNearBDP), for summarizing the
occurrence of motifs in peaks (summarizePatternInPeaks) and for
adding other IDs to annotated peaks or enrichedGO (addGeneIDs).
This package leverages the biomaRt, IRanges, Biostrings,
BSgenome, GO.db, multtest and stat packages

Lihua Julie Zhu

ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq,
ChIP-chip experiments or any experiments resulted in large
number of chromosome ranges.

TSS.zebrafish.Zv9 function

RangedData with slot start holding the start position of the gene, slot end holding the end position of the gene, slot rownames holding ensembl gene id and slot space holding the chromosome location where the gene is located. In addition, the following variables are included.
  <dl>
    <dt><code>strand</code></dt><dd>1 for positive strand and -1 for negative strand</dd> <dt><code>description</code></dt><dd>description of the gene</dd>
</dl> 

TSS.zebrafish.Zv9: TSS annotation for Danio rerio (Zv9) obtained from biomaRt

Description

Usage

Arguments

Format

Details

Examples