R/qtl sample data files

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These files contain sample QTL mapping data in several formats, so that the user may better understand how data may be formatted for import into R via the read.cross function. These are the same as the listeria data set included with the R/qtl package, which may be accessed by typing data(listeria). (The data come from Boyartchuk et al., Nat Genet 27:259-260, 2001.)

Please read the help file for read.cross; it explains all of the details.

Note: The code provided should work if you place the files in your R working directory; otherwise, replace "." with the correct directory (being careful, in Windows, to use either forward slashes ("/") or double-backslashes ("\\"), as a single backslash won't work). Alternatively, you may read these files directly from the web by using "http://www.rqtl.org/sampledata" in place of ".".


"csv" format
Data file:  listeria.csv
R code: listeria.a <- read.cross("csv", ".", "listeria.csv")
 
"csvr" format (rotated "csv")
Data file: listeria_rot.csv
R code: listeria.a2 <- read.cross("csvr", ".", "listeria_rot.csv")
 
"csvs" format (like "csv", but with separate files for phenotype and genotype data)
Genotypes: listeria_gen.csv
Phenotypes: listeria_phe.csv
R code: listeria.a3 <- read.cross("csvs", ".", "listeria_gen.csv", "listeria_phe.csv")
 
"csvsr" format (like "csvs", but with both files rotated)
Genotypes: listeria_gen_rot.csv
Phenotypes: listeria_phe_rot.csv
R code: listeria.a4 <- read.cross("csvsr", ".", "listeria_gen_rot.csv", "listeria_phe_rot.csv")
 
"mm" (MapMaker) format
Data file: listeria_raw.txt       ("raw" file containing both genotype and phenotype data)
Genetic map (ver 1): listeria_map.txt       (markers must be in order; map positions are not required)
Genetic map (ver 2): listeria_maps.txt      (as produced by MapMaker/Exp)
R code: listeria.b <- read.cross("mm", ".", "listeria_raw.txt", , "listeria_map.txt")
listeria.bb <- read.cross("mm", ".", "listeria_raw.txt", , "listeria_maps.txt")
 
"qtx" (Map Manager QTX) format
Data file: listeria.qtx
R code: listeria.c <- read.cross("qtx", ".", "listeria.qtx")
 
"qtlcart" (QTL Cartographer) format
Data file: listeria_qc_cro.txt
Genetic map: listeria_qc_map.txt
R code: listeria.d <- read.cross("qtlcart", ".", "listeria_qc_cro.txt", "listeria_qc_map.txt")


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