Commits

Author Commit Message Labels Comments Date
Giovanni Marco Dall'Olio
PLOTS: added a stub script to plot values by chromosomes, divided into facets. Other people have asked me to pass them a script for producing these type of plots
Giovanni Marco Dall'Olio
MERGE: merge conflicts from work done in the laptop
Giovanni Marco Dall'Olio
DOCS: added a Readme, including info on the published paper!!
Giovanni Marco Dall'Olio
ORANGE: tab-separated file for centralities
Giovanni Marco Dall'Olio
MERGE: merged the work done during Leipzig's course on orange with the latest change for the revision on BMC
Giovanni Marco Dall'Olio
ORANGE: added a kinophosphatome centralities file for orange
Giovanni Marco Dall'Olio
REFACT: changing the way how the interesting genes plots are generated
Giovanni Marco Dall'Olio
PLOTS: playing with scales in interesting-genes plots
Giovanni Marco Dall'Olio
PICKRELL: FIX: getting # of significant SNPs in the two datasets
Giovanni Marco Dall'Olio
PICKRELL: calculating which SNPs are significant in our data
Giovanni Marco Dall'Olio
FIX: correctly getting the cutoff values
Giovanni Marco Dall'Olio
PICKRELL: getting cutoffs for comparison against Pickrell
Giovanni Marco Dall'Olio
REFACT: adapting script for comparing against Pickrell to Fst
Giovanni Marco Dall'Olio
DATA: ADD: these are the correct files for Fst from Pickrell. Although I suspect that the names of the files may be inverted, as values in the pval file range from 0 to 5, while values in the other file range from 0 to 1.
Giovanni Marco Dall'Olio
DATA: included Fst by Pickrell This file contains 4 millions SNPs instead of 650.000, and it is not clear where do the other SNPs come from. Morevoer, it is not clear if the values included are Fst-global or Fst-pairwise (YRI-CEU).
Giovanni Marco Dall'Olio
MV: renamed script to compare iHS against Pickrell. stub for comparing Fst
Giovanni Marco Dall'Olio
MV: renamed script to produce figures 2 and 3
Giovanni Marco Dall'Olio
CLEANING: removing old files
Giovanni Marco Dall'Olio
FIX: improving the way SNPs from pickrell and our dataset are merged, increasing the number of matching SNPs
Giovanni Marco Dall'Olio
PLOTS: using 0-0.3 y axis limits for FST, and generating plots without ame and oce
Giovanni Marco Dall'Olio
DATA: removed out all controls
Giovanni Marco Dall'Olio
PICKRELL: extending the comparison to more genes (still not all the genes in the pathway)
Giovanni Marco Dall'Olio
PICKRELL: added spearman correlation test results. They are very good, specially after removing SSAFR, which is defined differently in Pickrell et al 2009
Giovanni Marco Dall'Olio
DATA: folder for comparison against pickrell
Giovanni Marco Dall'Olio
PICKRELL: merging Pickrell dataset with ours, plotting and testing correlation
Giovanni Marco Dall'Olio
PLOTS: adding plot of iHS values in Pickrell 2009. There are still some minor details to refine (order of pops, etc..)
Giovanni Marco Dall'Olio
DATA: SRC: new table of iHS values from Pickrell
Giovanni Marco Dall'Olio
REV: SRC: adapting code to read Pickrell data and merge with pathway annotation
Giovanni Marco Dall'Olio
DATA: downloaded iHS data from Pickrell et al 2009
Giovanni Marco Dall'Olio
ADD: script to compare against Pickrell data, derived from get_stat_by_snp_table.R
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