read.outcross {onemap} | R Documentation |
Imports data from a full-sib family derived from two outbred parents
and creates an object of class outcross
. Currently only one
format is supported.
read.outcross(dir, file)
dir |
directory where the input file is located. |
file |
the name of the input file which contains the data to be read. |
The only format currently supported is quite similar to that of
MAPMAKER/EXP
(Lincoln et al., 1993). The first line
contains two integers: the number of individuals and the number of
markers.
Next comes the genotype data for all markers. Each new marker is
initiated with a “*” (without the quotes) followed by the
marker name, without any space between them. Each marker name is
followed by the corresponding segregation type, which may be:
"A.1"
, "A.2"
, "A.3"
, "A.4"
, "B1.5"
,
"B2.6"
, "B3.7"
, "C.8"
, "D1.9"
,
"D1.10"
, "D1.11"
, "D1.12"
, "D1.13"
,
"D2.14"
, "D2.15"
, "D2.16"
, "D2.17"
or
"D2.18"
(without quotes) [see mrktype
and
Wu et al. (2002) for details].
Finally, after the segregation type comes the genotype data for the
corresponding marker. Depending on the segregation type, genotypes may
be denoted by ac
, ad
, bc
, bd
, a
,
ba
, b
, bc
, ab
and o
, in various
combinations. To make things easier, we have followed exactly
the notation used by Wu et al. (2002). Genotypes must be
separated by commas. Missing values are denoted by "-"
The example
directory in the package distribution contains
an example data file to be read with this function. Further
instructions can be found at the tutorial distributed along with this
package.
An object of class outcross
, i.e., a list with the following
components:
geno |
a matrix with character strings indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual. |
n.ind |
number of individuals. |
n.mar |
number of markers. |
segr.type |
a vector with the segregation type of each marker. |
Gabriel R A Margarido, gramarga@esalq.usp.br
Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
example
directory in the package source.
## Not run: outcr_data <- read.outcross(dir="work_directory",file="data_file.txt") ## End(Not run)