This repositary is used for generating the time-to-event phenotypes in UK Biobank based on PheCodes (using ICD9 and ICD10).
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The failure time was defined as the interval, rounded to the nearest full month, from their birth year and month to the diagnosis date of the relevant PheCode-specific PheCodes.
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Subjects with relevant PheCodes but without corresponding diagnosis dates were excluded from the analysis.
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Subjects without relevant PheCodes and without exclusion PheCodes as defined by the PheCode were classified as censored. For these subjects, the censoring time was defined as the interval, rounded to the nearest full month, from their birth year and month to the latest of the following: the most recent recorded diagnosis date of any PheCodes, the lost-to-follow-up date, or the recorded date of death.
data.table, tidyr, parallel, intervals, XML, RCurl, htmltab, bitops, stringr, and zoo,
Collect fields data of UKBB
output: ./data/FieldListing.txt
Create phenome and phecode files of UKBB
input:
UK Biobank main data (*.csv)
UK Biobank genome fam data (*.fam)
output:
./results/UKB_PHENOME_DESCRIPTION.txt
./results/UKB_PHENOME.txt
./results/UKB_PHENOME_ICD9_PHECODE_MAP.txt
./results/UKB_PHENOME_ICD10_PHECODE_MAP.txt
./results/UKB_PHENOME_UNMAPPED_ICD9_CODES.txt
./results/UKB_PHENOME_UNMAPPED_ICD10_CODES.txt
Map ICD9 and ICD10
input:
./results/UKB_PHENOME_UNMAPPED_ICD9_CODES.txt
./results/UKB_PHENOME_UNMAPPED_ICD10_CODES.txt
output:
/results/UKB_PHECODE_v1.2b1_ICD_Mapping.txt
Create time-to-event phenotypes
input:
UK Biobank main data (*.csv)
UK Biobank genome fam data (*.fam)
./data/FieldListing.txt
./results/UKB_PHECODE_v1.2b1_ICD_Mapping.txt
./results/UKB_PHENOME_DESCRIPTION.txt
./results/UKB_PHENOME.txt
output:
./phenotypes/*_pheSurv_useAttendTime.txt
https://github.com/umich-cphds/createUKBphenome https://github.com/atgu/ukbb_pan_ancestry/blob/master/create_phecode_mapping.R
This software is licensed under GPLv3.
