EVOLUTION-MANAGER

Edit File: README.txt

Sample data for the R/qtl package

These files contain sample data in several formats, so that the user
may better understand how data may be formatted for import via the
read.cross function.  These are the same as the "listeria" data
set included with the R/qtl package.

Note: Replace the "..." in the directory string to the appropriate
location of the sampledata directory (for example,
"/usr/local/lib/R/library/qtl" or "c:/R/rw1081/library/qtl").

1. "csv" format

File:

listeria.csv

Data import:

listeria.a <- read.cross("csv", ".../sampledata", "listeria.csv")

2. "csvr" format (rotated "csv")

File:

listeria_rot.csv

Data import:

listeria.a2 <- read.cross("csvr", ".../sampledata", "listeria_rot.csv")

3. "csvs" format (like "csv", but with separate files for phenotype
   and genotype data)

Files:

listeria_gen.csv         Genotype data
        listeria_phe.csv         Phenotype data

Data import:

listeria.a3 <- read.cross("csvs", ".../sampledata",
                                  "listeria_gen.csv", "listeria_phe.csv")

4. "csvsr" format (like "csvr", but both files are rotated)

Files:

listeria_gen_rot.csv     Genotype data
        listeria_phe_rot.csv     Phenotype data

Data import:

listeria.a4 <- read.cross("csvsr", ".../sampledata",
                                  "listeria_gen_rot.csv", 
                                  "listeria_phe_rot.csv")

5. "mm" (mapmaker) format

Files:

listeria_raw.txt   "raw" file (with genotype and phenotype data)
       listeria_map.txt    Genetic map information (markers must be in
                           order; map positions are not required)
       listeria_maps.txt   Genetic map information, as produced by 
                           Mapmaker/exp

Data import:

listeria.b <- read.cross("mm", ".../sampledata",
                                "listeria_raw.txt",,"listeria_map.txt")

listeria.bb <- read.cross("mm", ".../sampledata",
                                 "listeria_raw.txt",,"listeria_maps.txt")

6. "qtx" (Mapmanager QTX) format

File:

listeria.qtx

Data import:

listeria.c <- read.cross("qtx", ".../sampledata", "listeria.qtx")

7. "qtlcart" (QTL Cartographer) format

Files:

listeria_qc_cro.txt    Genotype/phenotype data
        listeria_qc_map.txt    Genetic map information

Data import:

listeria.d <- read.cross("qtlcart", ".../sampledata", 
                                 "listeria_qc_cro.txt", "listeria_qc_map.txt")

8. "karl" format

Files:

gen.txt    Genotype data
        phe.txt    Phenotype data
        map.txt    Genetic map information

Data import:

listeria.e <- read.cross("karl", ".../sampledata",
                                 genfile="gen.txt", phefile="phe.txt",
                                 mapfile="map.txt")

or just the following:

listeria.e <- read.cross("karl", ".../sampledata")