Description Usage Arguments References See Also
This script will take an R/qtl input data file, and
prepare it for input to shmootl. Possible prep actions include
resolving map sequence labels ('normseq'
), estimating a new
genetic map with the R/qtl function 'est.map'
(Broman
et al. 2003), jittering existing map positions with the
R/qtl function 'jittermap'
(Broman et al. 2003),
and replacing empty cells with an explicit missing value symbol
('replace.missing'
).
If no prep actions are specified, map sequence labels are normalised; a genetic map is estimated if not found, otherwise the existing map is jittered; and empty cells are replaced with an explicit missing value. If one or more prep actions are specified, only the specified actions will be applied. It is the responsibility of the user to ensure that any changes are valid for a given input file.
Aside from prep actions, other options include
'require.mapunit'
, which indicates if the input file
must contain explicit map units; and 'include.mapunit'
,
which indicates if explicit map units should be included in
the output file. Options 'error.prob'
and 'map.function'
are passed to the R/qtl function 'est.map'
, while option
'amount'
is passed to the R/qtl 'jittermap'
function.
1 2 3 4 |
datafile |
R/qtl CSV file [required] |
normseq |
normalise map sequence labels |
estimap |
estimate genetic map |
error.prob |
genotyping error rate |
map.function |
genetic map function |
jittermap |
jitter map positions |
amount |
jitter amount |
replace.missing |
make missing values explicit |
require.mapunit |
require map units in input |
include.mapunit |
include map units in output |
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)
Other pipeline functions: run_annoqtl
,
run_digest
, run_estimap
,
run_interptimes
,
run_makecross
, run_makegeno
,
run_pullmap
, run_pushmap
,
run_recode
, run_report
,
run_scanone
, run_scantwo
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