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author | mutantturkey <mutantturke@gmail.com> | 2012-09-19 09:54:39 -0400 |
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committer | mutantturkey <mutantturke@gmail.com> | 2012-09-19 09:54:39 -0400 |
commit | e8ad4e96614fea1d6605b7bbd5c2d1a332f5daa2 (patch) | |
tree | ef2929c463721a1301bc09f705faaab6675d24c4 /fly-tools/cci-calculator/README.markdown | |
parent | 5cc9a2db607ac074343d7f18e14c3bb187123530 (diff) |
added README, added ability to specify output folder, and use 10 folds default, and calculate the fold size instead of the inverse
Diffstat (limited to 'fly-tools/cci-calculator/README.markdown')
-rw-r--r-- | fly-tools/cci-calculator/README.markdown | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/fly-tools/cci-calculator/README.markdown b/fly-tools/cci-calculator/README.markdown new file mode 100644 index 0000000..065563c --- /dev/null +++ b/fly-tools/cci-calculator/README.markdown @@ -0,0 +1,30 @@ +== This is the least square solution CCI calulator == + +You'll need to run this in matlab, and have prepared your CSV's in advance. You +should have two CSV's. One csv should be all of your concatenated feature +vectors. One feature per column, columns, and as many rows as you have +specimen. The second CSV should include the actual CI data recorded and +calculated by the biologists. + +In matlab the command may look like this: (note you need to be in the directory +to call this) + + [x, e] = LeastSquareSolution('../input/ALL_FVs.csv','ALL_CIs.csv', +../output/); + +Alternatively you can run it without first invoking the compiler by running +this: + + matlab -r "LeastSquareSolution ALL_FV.csv ALL_CIs.csv ../output" + + +The ouput will an output specified, and will be in text files that are named +like this: Fold_1.txt Fold_2.txt etc. You will find it somewhat annoying to have +to concatenate all that data manually so here is a nice one-liner that allows +you to concatenate all of your data. For the number of specimen in each fold, +you need to setup your variables accordingly. + +If we have 21 specimen per fold, use number of folds + 2 for the head argument, +and the number of folds for the tail. This will give you proper results! + + for i in Fold_*.txt; do head $i -n 23 | tail -n 21 >> output.txt; echo $i; done; |