yeastAnno: Example datasets from Genominator
In Genominator: Analyze, manage and store genomic data

Description Usage Format Source See Also Examples

3 example datasets from Genominator; 2 contain annotation information from yeast and 1 contain actual data from yeast as well. A bigger dataset is available in the experimental data package yeastRNASeq.

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data(yeastAnno)
data(yeastAnno.sources)
data(chr1_yeast)

yeastAnno is a data frame with 7124 observations on the following 5 variables: chr, start, end, strand, gene_biotype.

yeastAnno.sources is a list with four components names ensembl.gene, ensembl.transcript, ucsc.sgdGene, ucsc.ensGene containing annotation on yeast from 2 different sources (Ensembl and UCSC), each sources has two different queries (one gene-level, one transcript-level). The annotation was obtained in January 2010 and should not be used for analysis.

chr1_yeast is a data frame containing mock data in yeast from two different samples (labelled mRNA_1 and mRNA_2), linked to distinct genomic locations. There may be several data values linked to each genomic location.

Ensembl and UCSC January 2010.

There is a discussion of the yeastAnno.sources in the withShortRead vignette.

data(yeastAnno)
head(yeastAnno)
data(yeastAnno.sources)
names(yeastAnno.sources)
head(yeastAnno.sources$ensembl.gene)
data(chr1_yeast)
head(chr1_yeast)