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f27c223bdd
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resolving merge conflicts dur to shoddy data
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2020-07-14 14:09:42 +01:00 |
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8dc2fa7326
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fixed white space prob with mcsm input with merge
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2020-07-14 14:07:23 +01:00 |
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5a2084ba11
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remove white space in colnames before mcsm format output
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2020-07-14 12:59:40 +01:00 |
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c0827b56cc
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finding discrepancy in merging or dfs,grrrr
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2020-07-13 18:31:29 +01:00 |
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da0c03c2e0
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trying to resolve copy warning in code
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2020-07-13 12:20:43 +01:00 |
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5655af42c0
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added sanity checks for or_kinship calcs
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2020-07-13 11:37:43 +01:00 |
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167b051ae7
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added sanity checks for or_kin
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2020-07-10 15:24:57 +01:00 |
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cb31c5c8f4
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refactoring or_kin script minor changes only
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2020-07-10 12:38:42 +01:00 |
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6cedc3c14d
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refactoring or_kin script minor changes only
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2020-07-10 12:37:41 +01:00 |
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4fd3462fc8
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added cleaned up af_or_calcs.R
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2020-07-09 15:55:16 +01:00 |
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7b50dc3a3a
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added consistent style scripts to format kd & rd values
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2020-07-09 14:08:27 +01:00 |
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08379c0def
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minor tidy up in foldx, mcsm and dssp scripts
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2020-07-09 14:04:16 +01:00 |
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44597ec563
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renamed mcsm_wrapper to run_mcsm
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2020-07-09 13:33:56 +01:00 |
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c0fa9e3904
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added dssp.py with refactored argeparse
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2020-07-09 12:58:55 +01:00 |
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6725f08829
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adding default dirs and filenames to argparse in foldx and mcsm
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2020-07-09 12:57:08 +01:00 |
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6961a9cdb3
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minor edits to format mcsm data like sorting df
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2020-07-09 11:15:56 +01:00 |
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8931441fa5
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ran foldx and mcsm (get) for 33k dataset
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2020-07-08 20:30:32 +01:00 |
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172fa18420
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modified extraction to be explicit for extracting nsSNP for specified gene
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2020-07-08 18:47:22 +01:00 |
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436125745d
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minor changes in data extraction
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2020-07-08 16:01:54 +01:00 |
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65e6b28d9e
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data extraction tidy up
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2020-07-08 13:26:33 +01:00 |
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e4328df255
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saving work for the day
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2020-07-07 18:31:14 +01:00 |
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8f460347b4
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adding clean files for rerrun 35k dataset
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2020-07-07 18:28:55 +01:00 |
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0973717287
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added script to combine all files in one
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2020-07-07 16:06:11 +01:00 |
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01ef04613a
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renamed files that combine dfs
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2020-07-07 15:46:13 +01:00 |
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56d1617561
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testing combining df script
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2020-07-03 19:23:23 +01:00 |
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b09c15004b
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stil fiddling iwth combining dfs
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2020-07-03 19:22:46 +01:00 |
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e0ba3108f6
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added fixme: for some necessary required changes
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2020-07-02 14:16:40 +01:00 |
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fb277a1484
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added combining funct & combining_mcsm_foldx script
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2020-07-01 16:41:58 +01:00 |
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973a1a33da
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refactor foldx pipeline to include:
* command-line args
* creating necessary dirs automagically
* code cleanup, syntax errors, etc etc
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2020-06-30 17:14:30 +01:00 |
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e8a66a7a94
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updated code and made it tidy
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2020-06-25 14:40:44 +01:00 |
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7032baa08d
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tidying script
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2020-06-25 13:12:09 +01:00 |
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cdb1ea1476
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updated ref dict to create separate dicts
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2020-06-24 14:10:39 +01:00 |
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27a656dba1
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added commonly used mutation format for missense muts in the gene_specific nssnp_info file
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2020-06-24 13:34:35 +01:00 |
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a9498f8e08
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combined and output all ors
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2020-06-23 17:34:54 +01:00 |
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d8b272b0ae
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script for calcuating various OR & output csv
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2020-06-23 13:07:29 +01:00 |
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c80c87235e
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further tidy for OR calcs
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2020-06-23 12:19:26 +01:00 |
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e3ae1c3a95
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tody scracth script for various OR calcs
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2020-06-23 11:57:51 +01:00 |
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263527f576
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all OR calcs using sapply and output as df
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2020-06-22 18:17:06 +01:00 |
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6b5ced65e5
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extracting other params from logistic
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2020-06-22 14:11:16 +01:00 |
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28e52d4194
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script to combine ors and afs
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2020-06-22 13:07:26 +01:00 |
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c98ca7c8ae
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script to combine all ors
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2020-06-19 14:43:23 +01:00 |
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07258120de
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renamed files & added or kinship link file
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2020-06-19 10:33:26 +01:00 |
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c36197d75e
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updated Af and OR calcs script with argeparse and minor tidyup
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2020-06-18 18:37:55 +01:00 |
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f9a8ed3dc7
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getopt and commandArgs examples, and AF/OR update to use getopt()
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2020-06-18 17:59:28 +01:00 |
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864f814e1b
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removed merging df for AF_OR
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2020-06-18 16:10:02 +01:00 |
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3d1536f2b6
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af and or calcs, not merging
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2020-06-18 15:57:25 +01:00 |
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c4f9e24007
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foramtting and adding or
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2020-06-18 13:55:45 +01:00 |
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b73c506587
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added AF_and OR calcs script and making it generic
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2020-06-17 19:36:34 +01:00 |
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2cebd338ba
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ran struc param analysis
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2020-06-17 19:36:02 +01:00 |
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96da4d8ed5
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inlcuded the revised master file for 35k isolates
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2020-06-16 11:39:11 +01:00 |
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