genomeDataRaw: Genome samples processed data

In derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Description

10kb region from chr21 processed for 31 RNA-seq samples described in genomeInfo. The TopHat BAM files are included in the package and this is the output of loadCoverage applied to it with cutoff=NULL. For more information check the example of loadCoverage.

Format

A list with two components.

coverage

is a DataFrame object where each column represents a sample.

position

is NULL because no bases were filtered.

References

1. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010 Apr.

2. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 2010 Mar.

See Also

loadCoverage, genomeInfo

derfinder documentation built on Dec. 20, 2020, 2 a.m.