welch16
2019-09-10 fad2d50d4084cd610692123903bbe72cb6abc2fc
2019-02-19 welch16
started notebook comparing snp sets
tree@ c07f49 commitdiff
2019-02-19 welch16
added tibble of the 313 brest cancer snps of Mavaddat et al
tree@ 9338ff commitdiff
2019-01-04 welch16
added a pair of snps that had to be manually curated, because they weren't ...
tree@ 38dd5a commitdiff
2018-12-19 welch16
updated results to include also large k runs for knn-impute
tree@ 4c97fa commitdiff
2018-12-18 welch16
wrote code to evaluate different imputation methods
tree@ 1e3403 commitdiff
2018-12-12 welch16
grouped levels from variables together to make the binarization a bit more ...
tree@ 6c880b commitdiff
2018-12-07 welch16
updated the cleaning code to amy and john's instructions
tree@ 4ceaad commitdiff
2018-11-30 welch16
wrote a report trying the re-engineer the algorithms used to call genotypes...
tree@ 2da5b3 commitdiff
2018-11-30 welch16
wrote a script to translate the plexseq genotype calls into the vcf format
tree@ a3ba04 commitdiff
2018-11-28 welch16
changed sample to person_id in mayo genotype data
tree@ f02cb3 commitdiff
2018-11-27 welch16
cleaned mayo data
tree@ 5fc844 commitdiff
2018-11-20 welch16
updated analysis by removing the substudy factor feature. The results appea...
tree@ afa3d2 commitdiff
2018-11-16 welch16
added other svm method comparison
tree@ ae452d commitdiff
2018-11-15 welch16
added explanation to slides
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2018-11-15 welch16
finish slides
tree@ 6967cc commitdiff
2018-11-14 welch16
updated some plots in the markdown file
tree@ 906ea8 commitdiff
2018-11-14 welch16
prior results of RFEST
tree@ 545c52 commitdiff
2018-11-14 welch16
added commands to run rfest separated by fold
tree@ 09abf2 commitdiff
2018-11-14 welch16
run again to removed unclass files
tree@ f6fb9d commitdiff
2018-11-14 welch16
removed person_id from feature files
tree@ f7f3c1 commitdiff
2018-11-13 welch16
added shuffle options to python codes to fix the low accuracy issue
tree@ ad9690 commitdiff
2018-11-13 welch16
adding more slides and changed priority to have mayo snps first
tree@ 615664 commitdiff
2018-11-13 welch16
updated genotype hierarchy to do mayo > plexseq1 > plexseq2
tree@ ca3e40 commitdiff
2018-11-13 welch16
added the set of snps that weren't listed in the grant
tree@ 3f0df3 commitdiff
2018-11-12 welch16
removed zero variance and near zero variance features from the test as thos...
tree@ c5f43a commitdiff
2018-11-12 welch16
removed family histore features except fam_hist as those features have litt...
tree@ dddaae commitdiff
2018-11-12 welch16
summarized the results of the baseline runs, and performed a screening of a...
tree@ 24f52c commitdiff
2018-11-08 welch16
added emca4 snps from irene, and all the ones that either were requested by...
tree@ 467e8f commitdiff
2018-11-07 welch16
adding a set of common samples to build datasets
tree@ ca6a6a commitdiff
2018-11-07 welch16
re-run to remove another issue of a person with name APRIL-MAY... in plexse...
tree@ f59438 commitdiff
2018-11-07 welch16
re-run rfest clean, added step to sample the FAIL samples from a Ber(maf) f...
tree@ a822ff commitdiff
2018-11-07 welch16
updated list to include some other variables that were not listed on niko's...
tree@ 885a3f commitdiff
2018-11-06 welch16
updated rfest datasets
tree@ 9139c6 commitdiff
2018-11-06 welch16
updated minor allele frequency computation
tree@ 3c6dba commitdiff
2018-11-06 welch16
reviewed the snp with repeated samples, and noticed that the tic-tac-toe pa...
tree@ 2d8862 commitdiff
2018-11-06 welch16
fixed the corrections provided by John Hampton
tree@ 3eb7ee commitdiff
2018-11-06 welch16
Added family history features to the sample
tree@ e133ca commitdiff
2018-11-05 welch16
Added a step in the code to remove failed snps. That way, we are only keepi...
tree@ 83b458 commitdiff
2018-11-02 welch16
added review for the snps that have a publication in the second sheet but n...
tree@ 71df9f commitdiff
2018-11-01 welch16
Started writing a notebook about cleaning the data for rfest
tree@ 199ea0 commitdiff
2018-11-01 welch16
wrote a script to parse data into rfest required format
tree@ 08ef52 commitdiff
2018-10-31 welch16
added table with the snps from the grant proposal
tree@ 07f161 commitdiff
2018-10-26 welch16
Besides following Niko's processing steps, I added a features to the variab...
tree@ e1a770 commitdiff
2018-10-24 welch16
moved the dbSNP calls to metadata folder
tree@ aea5b1 commitdiff
2018-10-24 welch16
added query call from the ncbi api for all our snps to clean the alleles ac...
tree@ 714c47 commitdiff
2018-10-23 welch16
added instruction to convert all tibble names to lowercase
tree@ 668a05 commitdiff
2018-10-23 welch16
clean metadata fixed to check all snps and not only the ones of plexseq2
tree@ e40911 commitdiff
2018-10-22 welch16
fixed: mayo genotypes were coded differently for homozygous cases than plex...
tree@ c4fe47 commitdiff
2018-10-19 welch16
added suffix to file
tree@ 99c65c commitdiff
2018-10-19 welch16
created survey and breast density pre-files and files indicating which data...
tree@ ad0242 commitdiff
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