encodeTP53


	The data contains gene expression and transcript annotations in the region of the human TP53 gene (region (chr17:7,560,001-7,610,000 from the Human February 2009 (GRCh37/hg19) genome assembly), 
	which is part of the long RNA-seq data generated by ENCODE/Cold Spring Harbor Lab, containing 2 cell types (GM12878 and K562) with 2 replicates each.
	
	The alignment files were pulled from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/). 	
	And subsequently reads were counted in each non-overlapping 25bp window for the region (chr17:7,560,001-7,610,000). The example code to generate this count <code>GRanges</code> is available in the vignette.
	
	The regional annotation of TP53 RNAs isoforms were derived from the ENCODE Gene Annotations (GENCODE), sub-setted to only isoforms of TP53 gene.
	<a href="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGencodeV4/wgEncodeGencodeManualV4.gtf.gz)">http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGencodeV4/wgEncodeGencodeManualV4.gtf.gz)</a>.<p></p><p>	This dataset is used in the package vignette to illustrate a use case of transcript detection. 
</p>

datasets

data

In this package, a Hidden Semi Markov Model (HSMM) and one
homogeneous segmentation model are designed and implemented for
segmentation genomic data, with the aim of assisting in
transcripts detection using high throughput technology like
RNA-seq or tiling array, and copy number analysis using aCGH or
sequencing.

Yang Du

biomvRCNS

Copy Number study and Segmentation for multivariate biological
data

encodeTP53 function

Containing two <code>GRanges</code> objects, one for the sample count and one for the regional annotation of gene TP53

Format

The data contains gene expression and transcript annotations in the region of the human TP53 gene (region (chr17:7,560,001-7,610,000 from the Human February 2009 (GRCh37/hg19) genome assembly), 
	which is part of the long RNA-seq data generated by ENCODE/Cold Spring Harbor Lab, containing 2 cell types (GM12878 and K562) with 2 replicates each.
	
	The alignment files were pulled from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/). 	
	And subsequently reads were counted in each non-overlapping 25bp window for the region (chr17:7,560,001-7,610,000). The example code to generate this count <code>GRanges</code> is available in the vignette.
	
	The regional annotation of TP53 RNAs isoforms were derived from the ENCODE Gene Annotations (GENCODE), sub-setted to only isoforms of TP53 gene.
	<url>http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeGencodeV4/wgEncodeGencodeManualV4.gtf.gz)</url>.

	This dataset is used in the package vignette to illustrate a use case of transcript detection.

encodeTP53: mapped RNA-seq data from ENCODE

Description

Arguments

Format

References