ensembl.map {qtl} | R Documentation |
Opens an RODBC connection to a core database of EnsEMBL to retrieve physical positions of for markers.
ensembl.map (cross, dsn="ensembl_pub_mouse",user="anonymous",password="", distance=c("physical","genetic"),map, dbinterface=c("mysql","odbc"), trace=FALSE)
cross |
An object of class cross . See
read.cross for details. |
dsn |
Name of EnsEMBL database in odbc configuration or the group in .my.cnf. 'ensembl_pub_mouse' is the default name for the public installation of ensembl mouse data. |
user |
User name for connection to EnsEMBL database. 'anonymous' for accessing the public database on ensembldb.ensembl.org is the default. |
password |
password for connection to EnsEMBL database. The empty password is the default for connecting to the public EnsEMBL server. |
distance |
Selector of phyiscal position on chromosome ( in base pairs, default) and the genetic distance (centiMorgan or centiRays). |
map |
The map according to which the genetic distance was determined may be selected. This is not yet implemented. |
dbinterface |
Select either "odbc" or "mysql" as database interface with "mysql" being the default. |
A map
object; a list whose components (corresponding to
chromosomes) are either vectors of marker positions (in bp) or
matrices with two rows of sex-specific marker positions.
Karl W Broman, kbroman@jhsph.edu, Steffen Möller, moeller@pzr.uni-rostock.de
Lange, K. (1999) Numerical analysis for statisticians. Springer-Verlag. Sec 23.3.
Rabiner, L. R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257–286.
Lander, E. S. and Green, P. (1987) Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84, 2363–2367.
Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E. (2003) Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31:38-42.
est.map
, plot.map
, replace.map
,
est.rf
, http://www.ensembl.org
, http://www.mysql.com
data(hyper) newmap <- ensembl.map(hyper) logliks <- sapply(newmap, attr, "loglik") plot.map(hyper, newmap) hyper <- replace.map(hyper, newmap)