Open jaamarks opened 4 years ago
dbGaP_phenotypeDS_03292013.txt
This sheet was found at:
//RTPNFIL02/eojohnson/HIV/hiv_data/UHS/UHS dbGaP submission/FinalPhenotypeFiles_dbGaP/Updated_030413/Updated_032913/dbGaP_phenotypeDS_03292013.txt
subjid | sampid | consent | affection_status | hivstat | ViralLoad_cperml | ViralLoad_Log10 | sex | gwassex | race | age | age_cat | year | year_cat | lca_groupá | mpartners | stis | anal | needleshare | sexwork | site | cluster | final_analysis |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HHG4751 | 328952 | 1 | 1 | 1 | 35000 | 4.54 | 1 | 1 | 1 | 44 | 1 | 1998 | 2 | 3 | 0 | 1 | 0 | 0 | 0 | 2 | 271 | 1 |
HHG6687 | 407014 | 1 | 2 | 0 | -99999 | -99999 | 1 | -2 | 2 | 37 | 0 | 1994 | 1 | 1 | 0 | -99999 | 0 | -99999 | 1 | 2 | -99999 | 1 |
HHG7140 | 513323 | 1 | 1 | 1 | 1060 | 3.03 | 2 | 2 | 2 | 42 | 1 | 1992 | 1 | 1 | 0 | 0 | 0 | -99999 | 1 | 2 | 220 | 1 |
HHG7939 | 448818 | 1 | 2 | 0 | -99999 | -99999 | 1 | -2 | 2 | 38 | 1 | 1997 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | -99999 | 1 |
HHG1973
not in this original submission.//RTPNFIL02/eojohnson/HIV/hiv_data/UHS/UHS dbGaP submission/FinalPhenotypeFiles_dbGaP/Updated_030413/dbGaP_phenotypeDD_02072013.txt
subjid | hivstat | age_hiv | viralload_cperml | viralload_log10 | sex_selfreport | gwassex | ancestry_selfreport | age | surveyyear | lca_group | mpartners | stis | anal | needleshare | sexwork | site | heroin_ever | heroin_ever_inj | opioid_ever | opioid_ever_inj | totopioid_ever | heroin_age_ons | opioid_age_ons | totopioid_age_ons | heroin_inj_30d | heroin_non_30d | opioid_inj_30d | opioid_non_30d | totopioid_inj_30d | totopioid_non_30d | totopioid_tot_30d | heroin_case | opioid_case | totopioid_case | inj_ever | inj_freq | inj_case | inj_age_ons | coc_ever | coc_ever_inj | amphet_ever | amphet_ever_inj | sed_ever | sed_ever_inj | mj_ever | coc_age_ons | amphet_age_ons | sed_age_ons | mj_age_ons | cocaine_inj_30d | cocaine_non_30d | totcoc_30d | amphet_inj_30d | amphet_non_30d | totamphet_30d | mj_30d | totcoc_case | totamphet_case | mj_case |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HHG4751 | 1 | 43 | 35000 | 5 | 2 | 1 | 1 | 43 | 1998 | 3 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 19 | 20 | 19 | 49 | 0 | 0 | 49 | 0 | 49 | 1 | 0 | 1 | 1 | 57 | 1 | 19 | 1 | 1 | 1 | 1 | 1 | -8 | 1 | 19 | -99999 | -99999 | -99999 | 0 | 0 | 0 | 8 | 3 | 11 | 0 | 1 | |||
HHG6687 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 36 | 1994 | 1 | 0 | -99999 | 0 | -99999 | 1 | 1 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | -8 | 30 | 15 | 0 | 0 | 30 | 15 | 45 | 1 | 0 | 1 | 1 | 30 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | 1 | -99999 | -99999 | -99999 | 14 | 0 | 45 | 45 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | |
HHG7140 | 1 | 45 | 1060 | 3 | 1 | 2 | 2 | 45 | 1992 | 1 | 0 | 0 | 0 | -99999 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 21 | 21 | 75 | 0 | 0 | 75 | 0 | 75 | 1 | 0 | 1 | 1 | 125 | 1 | 21 | 1 | 1 | 1 | 1 | -8 | -8 | -99999 | 30 | -99999 | -99999 | -99999 | 0 | 30 | 30 | 50 | 0 | 50 | 1 | 1 | ||||
HHG7939 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 36 | 1997 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | -8 | 120 | 30 | 0 | 0 | 120 | 30 | 150 | 1 | 0 | 1 | 1 | 120 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | 1 | -99999 | -99999 | -99999 | 12 | 0 | 20 | 20 | 0 | 0 | 0 | 99 | 1 | 0 | 1 | |
HHG1973 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 41 | 1993 | 1 | 1 | 1 | 0 | 0 | 1 | 2 | 1 | 1 | 0 | 0 | 1 | 31 | 31 | 24 | 0 | 0 | 0 | 24 | 0 | 24 | 1 | 0 | 1 | 1 | 24 | 1 | 32 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 33 | 28 | 0 | 27 | 27 | 0 | 0 | 0 | 1 | 0 |
HHG4751 328952@1054755694 HHG6687 407014@1054753316 HHG7140 513323@1054752755 HHG7939 448818@1054697882 HHG1973 942966@1054697675
iid | hiv | age | gender | PC1 | PC9 | PC10 | |
---|---|---|---|---|---|---|---|
328952@1054755694_328952@1054755694 | 1 | 43 | 1 | -0.002 | 0.0132 | 5.00E-04 | 0.0044 |
407014@1054753316_407014@1054753316 | 0 | 36 | 1 | 0.0111 | 0.0031 | 0.001 | 0.0031 |
513323@1054752755_513323@1054752755 | 1 | 45 | 0 | -0.011 | 0.0189 | 0.006 | -2.00E-04 |
448818@1054697882_448818@1054697882 | 0 | 36 | 1 | 0.0079 | -0.0096 | -0.0077 | 0.0223 |
942966@1054697675_942966@1054697675 | 0 | 41 | 1 | 0.0048 | 0.0019 | -5.00E-04 | 5.00E-04 |
subjid | hivstat | age_hiv | viralload_cperml | viralload_log10 | sex_selfreport | gwassex | ancestry_selfreport | age | surveyyear | lca_group | mpartners | stis | anal | needleshare | sexwork | site | heroin_ever | heroin_ever_inj | opioid_ever | opioid_ever_inj | totopioid_ever | heroin_age_ons | opioid_age_ons | totopioid_age_ons | heroin_inj_30d | heroin_non_30d | opioid_inj_30d | opioid_non_30d | totopioid_inj_30d | totopioid_non_30d | totopioid_tot_30d | heroin_case | opioid_case | totopioid_case | inj_ever | inj_freq | inj_case | inj_age_ons | coc_ever | coc_ever_inj | amphet_ever | amphet_ever_inj | sed_ever | sed_ever_inj | mj_ever | coc_age_ons | amphet_age_ons | sed_age_ons | mj_age_ons | cocaine_inj_30d | cocaine_non_30d | totcoc_30d | amphet_inj_30d | amphet_non_30d | totamphet_30d | mj_30d | totcoc_case | totamphet_case | mj_case |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HHG4751 | 1 | 43 | 35000 | 5 | 2 | 1 | 1 | 43 | 1998 | 3 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 19 | 20 | 19 | 49 | 0 | 0 | 49 | 0 | 49 | 1 | 0 | 1 | 1 | 57 | 1 | 19 | 1 | 1 | 1 | 1 | 1 | -8 | 1 | 19 | -99999 | -99999 | -99999 | 0 | 0 | 0 | 8 | 3 | 11 | 0 | 1 | |||
HHG6687 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 36 | 1994 | 1 | 0 | -99999 | 0 | -99999 | 1 | 1 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | -8 | 30 | 15 | 0 | 0 | 30 | 15 | 45 | 1 | 0 | 1 | 1 | 30 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | 1 | -99999 | -99999 | -99999 | 14 | 0 | 45 | 45 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | |
HHG7140 | 1 | 45 | 1060 | 3 | 1 | 2 | 2 | 45 | 1992 | 1 | 0 | 0 | 0 | -99999 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 21 | 21 | 75 | 0 | 0 | 75 | 0 | 75 | 1 | 0 | 1 | 1 | 125 | 1 | 21 | 1 | 1 | 1 | 1 | -8 | -8 | -99999 | 30 | -99999 | -99999 | -99999 | 0 | 30 | 30 | 50 | 0 | 50 | 1 | 1 | ||||
HHG7939 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 36 | 1997 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | -8 | 120 | 30 | 0 | 0 | 120 | 30 | 150 | 1 | 0 | 1 | 1 | 120 | 1 | 1 | -8 | -8 | -8 | -8 | -8 | 1 | -99999 | -99999 | -99999 | 12 | 0 | 20 | 20 | 0 | 0 | 0 | 99 | 1 | 0 | 1 | |
HHG1973 | 0 | -99999 | -99999 | -99999 | 2 | -99999 | 2 | 41 | 1993 | 1 | 1 | 1 | 0 | 0 | 1 | 2 | 1 | 1 | 0 | 0 | 1 | 31 | 31 | 24 | 0 | 0 | 0 | 24 | 0 | 24 | 1 | 0 | 1 | 1 | 24 | 1 | 32 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 33 | 28 | 0 | 27 | 27 | 0 | 0 | 0 | 1 | 0 |
HHG4751 328952@1054755694 HHG6687 407014@1054753316 HHG7140 513323@1054752755 HHG7939 448818@1054697882 HHG1973 942966@1054697675
iid | hiv | age | gender | PC1 | PC9 | PC10 | |
---|---|---|---|---|---|---|---|
328952@1054755694_328952@1054755694 | 1 | 43 | 1 | -0.002 | 0.0132 | 5.00E-04 | 0.0044 |
407014@1054753316_407014@1054753316 | 0 | 36 | 1 | 0.0111 | 0.0031 | 0.001 | 0.0031 |
513323@1054752755_513323@1054752755 | 1 | 45 | 0 | -0.011 | 0.0189 | 0.006 | -2.00E-04 |
448818@1054697882_448818@1054697882 | 0 | 36 | 1 | 0.0079 | -0.0096 | -0.0077 | 0.0223 |
942966@1054697675_942966@1054697675 | 0 | 41 | 1 | 0.0048 | 0.0019 | -5.00E-04 | 5.00E-04 |
Version 002 of phenotype files
dbGaP_phenotypeDD_20191211.xlsx dbGaP_phenotypeDS_20191211.txt
Issues
s3://rti-heroin/hiv_all_merged_with_uhs_all_phenotype_data_08282017.csv.gz
, in the GWAS phenotype, or in the observed genotype data.