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== Results Sharing | == Results Sharing == | ||
The following variables should be included when sharing imputed results for meta-analysis; large files can be shared among small groups via secure file transfer site (as described in [[ResultsSharing|Results Sharing]]). Many working groups use | The following variables should be included when sharing imputed results for meta-analysis; large files can be shared among small groups via secure file transfer site (as described in [[ResultsSharing|Results Sharing]]). Many working groups use Google Drive, a secure web-based file-sharing system in partnership with by the University of Washington's computing group. The service has ample storage space for large files and limits access to a select group identified by [http://www.washington.edu/lst/news/2012/google-login Google Account] IDs. | ||
<br> ShareSpace Access is arranged via working groups. New members who expect to need access to these sites should create a Google Account ID: [https://accounts.google.com/SignUp?service=mail&continue=http | <br/>ShareSpace Access is arranged via working groups. New members who expect to need access to these sites should create a Google Account ID: [https://accounts.google.com/SignUp?service=mail&continue=http://mail.google.com/mail/<mpl=default create a new Google Account]. | ||
== File Formats == | == File Formats == | ||
Results should be shared as plain text files, with the following variable names: | Results should be shared as plain text files, with the following variable names: | ||
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|- | |- | ||
| '''chr''' | | '''chr''' | ||
| chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.<br> | | chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.<br/> | ||
|- | |- | ||
| '''position''' | | '''position''' | ||
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|- | |- | ||
| '''beta''' | | '''beta''' | ||
| beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available<br> | | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''SE''' | | '''SE''' | ||
| standard error of beta estimate, to at least 5 decimal places -- “NA” if not available<br> | | standard error of beta estimate, to at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''pval''' | | '''pval''' | ||
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|- | |- | ||
| '''AF_coded_all''' | | '''AF_coded_all''' | ||
| allele frequency for the coded allele -- “NA” if not available<br> | | allele frequency for the coded allele -- “NA” if not available<br/> | ||
|- | |- | ||
| '''HWE_pval''' | | '''HWE_pval''' | ||
| exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed<br> | | exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed<br/> | ||
|- | |- | ||
| '''callrate''' | | '''callrate''' | ||
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''Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.'' | ''Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.'' | ||
<br/>For gene-environment interaction analyses, the following variables should be included: | |||
For gene-environment interaction analyses, the following variables should be included: | |||
{| width="800" border="1" class="prettytable" | {| width="800" border="1" class="prettytable" | ||
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|- | |- | ||
| '''chr''' | | '''chr''' | ||
| chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.<br> | | chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.<br/> | ||
|- | |- | ||
| '''position''' | | '''position''' | ||
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|- | |- | ||
| '''beta''' | | '''beta''' | ||
| beta estimate from additive interaction term, at least 5 decimal places -- “NA” if not available<br> | | beta estimate from additive interaction term, at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''SE''' | | '''SE''' | ||
| standard error of beta estimate, to at least 5 decimal places -- “NA” if not available<br> | | standard error of beta estimate, to at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''pval''' | | '''pval''' | ||
| p-value of interaction test statistic, here just as a double check -- “NA” if not available<br> | | p-value of interaction test statistic, here just as a double check -- “NA” if not available<br/> | ||
|- | |- | ||
| '''df.t''' | | '''df.t''' | ||
| degrees of freedom estimate for t reference distribution for interaction term -- “NA” if not available<br> | | degrees of freedom estimate for t reference distribution for interaction term -- “NA” if not available<br/> | ||
|- | |- | ||
| '''pval.t''' | | '''pval.t''' | ||
| p-value of interaction test statistic, using t reference distribution, here just as a double check -- “NA” if not available<br> | | p-value of interaction test statistic, using t reference distribution, here just as a double check -- “NA” if not available<br/> | ||
|- | |- | ||
| '''beta.main''' | | '''beta.main''' | ||
| beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available<br> | | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''SE.main''' | | '''SE.main''' | ||
| standard error of beta.main estimate, to at least 5 decimal places -- “NA” if not available<br> | | standard error of beta.main estimate, to at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''pval.main''' | | '''pval.main''' | ||
| p-value of main test statistic, here just as a double check -- “NA” if not available<br> | | p-value of main test statistic, here just as a double check -- “NA” if not available<br/> | ||
|- | |- | ||
| '''covar.main.inter''' | | '''covar.main.inter''' | ||
| covariance between beta and beta.main, to at least 5 decimal places -- “NA” if not available<br> | | covariance between beta and beta.main, to at least 5 decimal places -- “NA” if not available<br/> | ||
|- | |- | ||
| '''AF_coded_all''' | | '''AF_coded_all''' | ||
| allele frequency for the coded allele -- “NA” if not available<br> | | allele frequency for the coded allele -- “NA” if not available<br/> | ||
|- | |- | ||
| '''HWE_pval''' | | '''HWE_pval''' | ||
| exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed<br> | | exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed<br/> | ||
|- | |- | ||
| '''callrate''' | | '''callrate''' | ||
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''Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.'' | ''Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.'' | ||
[[Category:Analysis Guidelines]] [[Category:Analysis]] | |||
[[Category:Analysis Guidelines]] | |||
[[Category:Analysis]] |
Latest revision as of 22:41, 21 June 2016
Results Sharing
The following variables should be included when sharing imputed results for meta-analysis; large files can be shared among small groups via secure file transfer site (as described in Results Sharing). Many working groups use Google Drive, a secure web-based file-sharing system in partnership with by the University of Washington's computing group. The service has ample storage space for large files and limits access to a select group identified by Google Account IDs.
ShareSpace Access is arranged via working groups. New members who expect to need access to these sites should create a Google Account ID: create a new Google Account.
File Formats
Results should be shared as plain text files, with the following variable names:
variable name | description |
SNPID | SNP ID as rs number |
chr | chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers. |
position | physical position for the reference sequence (indicate build 35/36 in readme file) |
coded_all | coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G) |
noncoded_all | the other allele |
strand_genome | + or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on |
beta | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available |
SE | standard error of beta estimate, to at least 5 decimal places -- “NA” if not available |
pval | p-value of test statistic, here just as a double check -- “NA” if not available |
AF_coded_all | allele frequency for the coded allele -- “NA” if not available |
HWE_pval | exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed |
callrate | genotyping callrate after exclusions |
n_total | total sample with phenotype and genotype for SNP |
imputed | 1/0 coding; 1=imputed SNP, 0=if directly typed |
used_for_imp | 1/0 coding; 1=used for imputation, 0=not used for imputation |
oevar_imp | observed divided by expected variance for imputed allele dosage |
Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.
For gene-environment interaction analyses, the following variables should be included:
variable name | description |
SNPID | SNP ID as rs number |
chr | chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers. |
position | physical position for the reference sequence (indicate build 35/36 in readme file) |
coded_all | coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G) |
noncoded_all | the other allele |
strand_genome | + or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on |
beta | beta estimate from additive interaction term, at least 5 decimal places -- “NA” if not available |
SE | standard error of beta estimate, to at least 5 decimal places -- “NA” if not available |
pval | p-value of interaction test statistic, here just as a double check -- “NA” if not available |
df.t | degrees of freedom estimate for t reference distribution for interaction term -- “NA” if not available |
pval.t | p-value of interaction test statistic, using t reference distribution, here just as a double check -- “NA” if not available |
beta.main | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available |
SE.main | standard error of beta.main estimate, to at least 5 decimal places -- “NA” if not available |
pval.main | p-value of main test statistic, here just as a double check -- “NA” if not available |
covar.main.inter | covariance between beta and beta.main, to at least 5 decimal places -- “NA” if not available |
AF_coded_all | allele frequency for the coded allele -- “NA” if not available |
HWE_pval | exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed |
callrate | genotyping callrate after exclusions |
n_total | total sample with phenotype and genotype for SNP |
n_exposed | (DICHOTOMOUS EXPOSURE ONLY) number in sample exposed to environmental variable of interest [in longitudinal data, estimated number of independent observations that are exposed] |
imputed | 1/0 coding; 1=imputed SNP, 0=if directly typed |
used_for_imp | 1/0 coding; 1=used for imputation, 0=not used for imputation |
oevar_imp | observed divided by expected variance for imputed allele dosage |
Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.