This software is provided free with absolutely no guarantees.
R CMD install bagphenotype.library.tar.gz
tar -zxf bagphenotype.tgz
||"0" or "1", meaning false or true, respectively.|
||A directory name||
"additive" for the additive genetic model
"full" for the additive + dominance genetic model
"additive,full" or "both" for both additive and full model (fit separately)
"1" for the models specified in the
The options and arguments following
bagphenotype.pl configfile ...
--nomenuconfigand create any directories necessary for any other options specified.
--memory 100then bagphenotype will load necessary markers into memory until the total R object size exceeds 100Mb. This is only useful (and typically only implemented) for those parts of the analysis where it is expected that the same marker could be loaded from disk multiple times during a Rscript run. It is not useful for when it is expected that each marker will be loaded only once. For example it would not be useful for:
- Write a "complete" version of the config file to configfile.update in the directory specified by
--outdir. If the config file specified a
menu.file, the information from the menu file is incorporated in the updated config file. When a non-blank field occurs in both config and menu files, the value in the config file is used. This assumes the menu file to act as a template file containing common options, which the config file fills in or/and overrides.
- Do single locus null simulations of the specified genetic models and calculate quantiles. In each null simulation, fake phenotypes are generated by parametric bootstrapping from the fitted null model.
- Specify directory for all output. This is ./ by default.
- For each specified model, generate a file of high scoring "peak" loci from the single locus scans. The behavior of this option depends on the
peak.separationfield of the config file.
- Do single locus permutation tests of the specified genetic models and calculate quantiles.
- Plot available single locus scans and significance thresholds.
- Plot available single locus scans, significance thresholds and multilocus scans. This plots in a slightly different format from the
- Perform resample model averaging of multilocus models using the specified genetic model.
- Specify directory for output of single locus scans, null scans and permutation scans. This will be subdirectory of the directory specified by
chromosomes 1 2 3 X".
phenotypefilled in as
GlucoseAUC_model1, and GlucoseAUC_second.config with the
phenotypefilled in as
GlucoseAUC_model2. Running bagphenotype on both configs in the same directory would yield two separate sets of results files prefixed with GlucoseAUC_model1 and GlucoseAUC_model2 respectively.
Q: Are the thresholds in the *.thresh.permscan.additive files generated empirically or from the extreme value distribution? If the latter, how does one get from the parameter estimates in pheno.gev.permscan to the threshold values?
A: No, they're calculated from the GEV (of which the EVD is an example). Bagphenotype puts maxima from the permutations in the PERMUTATIONS/ directory. There is one such file for each chromosome and it lists the maximum logP for the chromosome for each permutation. Bagphenotype then reads all these chromosome files, and for each permutation picks the maximum logP across chromosomes. Bagphenotype then fits these to a generalized extreme value distribution using the R library evd (function fgev). This distribution has three parameters, and the estimates of those parameters are written to the .gev.additive file. Bagphenotype then plugs those parameter estimates into the R function qgev to get the upper 0.05 quantile of that fitted distribution (and the 0.2 quantile, or whatever is asked for in the config file). All the information you need to calculate your own thresholds is in the .gev.additive file, provided you're happy with using the qgev() function.