genomeData: 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. 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 a logical Rle with the positions of the chromosome that passed a cutoff of 0.

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.