genomeInfo: Genome samples information

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

Genome samples information

Description

Information for the 31 samples downloaded from the Short Read Archive from studies comparing CEU and YRI populations. This data is used to specify the adjustment variables in calculateStats. The data is sorted according to the BAM files identifiers. Reads were 36bp long.

Format

A data.frame with 5 columns:

run

The short name used to identify the sample BAM file.

library.layout

Whether it was a single-end library or a paired-end library.

hapmap.id

The HapMap identifier of the person sequenced. Note that some were sequenced more than once.

gender

Whether the person sequence is a female or a male.

pop

The population the person belongs to.

Details

The samples are from:

10

unrelated females from the YRI population.

5

unrelated females from the CEU population.

5

unrelated males (unrelated to the females too) from the CEU population.

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

genomeData, calculateStats

lcolladotor/derfinder documentation built on May 10, 2023, 11:07 p.m.