ATH.coord: Data on probes coordinates

In eqtl: Tools for analyzing eQTL experiments: A complementary to Karl Broman's 'qtl' package for genome-wide analysis

Description

Data for the physical coordinates of A. thaliana GST (probes).

Usage

data(ATH.coord)

Format

A data frame with 487 observations with the following 4 variables representing GST genomic coordinates:

etrait.name

a factor with GST names as levels

chr

an integer vector corresponding to the chromosomes.

start

an integer vector corresponding to the GST start location in base pair.

stop

an integer vector corresponding to the GST stop location in base pair.

Details

The CATMA microarray, composed of Gene Sequence Tag ( GST ) referenced below, correspond to the expression phenotypes measured on their related cross object (here, they describes the seed10 object). Usually, all expression traits are not taken into account within a QTL analysis, therefore this list could contain more traits than the ones phenotyped within the cross object. On the other hand, every phenotype analysed must be found within ATH.coord data frame. Please note that ATH.coord contains the physical locations values of an anonymized GST sample taken from true CATMA 2 data which originaly contains 30334 GST. The complete data is available on from the TAIR or CATdb websites.

Source

Jean-Pierre Renou and Alain Lecharny (CATdb a Complete Arabidopsis Transcriptome database)(http://urgv.evry.inra.fr/CATdb)
The Arabidopsis Information Ressource (TAIR) (http://www.arabidopsis.org)

References

Crowe M.L. et al., (2003) CATMA A complete Arabidopsis GST database. Nucleic Acids Res 31:156-158.

Examples

data(ATH.coord);

eqtl documentation built on May 2, 2019, 5:42 a.m.