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keller_and_evans_lab:gscan [2016/09/12 14:53] scott /* Phenotype definitions and analysis plan */ |
keller_and_evans_lab:gscan [2019/10/28 15:59] lessem ↷ Page moved from gscan to keller_and_evans_lab:gscan |
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======= GSCAN GWAS ======= | ======= GSCAN GWAS ======= | ||
+ | |||
+ | |||
+ | ====== Workgroups ====== | ||
+ | |||
+ | * **Phenotype workgroup: | ||
+ | * **Analysis workgroup: | ||
Line 56: | Line 62: | ||
- | ====== [[gscan_db_ga_p]] ====== | + | ====== [[gscan_db_ga_p]] |
Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[gscan_db_ga_p]] page. | ||
- | ====== GSCAN use of UKBiobank | + | ======= GSCAN Sequencing ======= |
- | More information about the files used for [[uk_biobank|UKBiobank are here]]. In brief, we used the UK10K + 1kgp3 imputed vcfs provided by UKBionank and added in dosages w/ this python script: | ||
- | import gzip, argparse, re, os, datetime | + | ====== TOPMed ====== |
- | from subprocess import Popen, PIPE | + | |
- | def add_dosage(pair): | + | We hope to update this section with detailed descriptions of how we have conducted phenotype derivations for each TOPMed cohort to which we have access to raw data. |
- | a, b = pair | + | |
- | probs = b.split(b',' | + | |
- | dose = float(probs[1]) + (float(probs[2]) * 2) | + | |
- | return a + b':' | + | |
- | def gziplines(fname): | + | * For now, the R scripts to go from source phenotype file to eventual derived phenotype is located here: |
- | f = Popen([' | + | |
- | | + | |
- | yield line | + | |
- | parser = argparse.ArgumentParser() | + | * We're tracking analyses in [[https:// |
- | parser.add_argument(' | + | |
- | args = parser.parse_args() | + | |
- | flag = False | ||
- | for line in gziplines(args.inputVCF): | + | ===== Phenotype definitions and analysis plan for external studies |
- | if line.startswith(b'#' | + | |
- | os.write(1, line.rstrip() + b' | + | |
- | if not flag: | + | |
- | os.write(1, b'## | + | |
- | os.write(1, b'## | + | |
- | str(datetime.datetime.now()).encode(' | + | |
- | flag = True | + | |
- | else: | + | |
- | elements | + | |
- | first8 | + | |
- | genotypes | + | |
- | form = b' | + | |
- | genotypes_split = zip(genotypes[:: | + | Phenotype definitions and analysis plans for the TOPMed studies are {{file_topmed_smoking_analysis_plan-v0_2.docxcontained |
- | try: | + | |
- | dose_genos = [add_dosage(pair) | + | |
- | except (ValueError, | + | |
- | os.write(2, " | + | |
- | os.write(2, line + " | + | |
- | raise e | + | |
- | os.write(1, b' | + | |
+ | The list of dbGaP studies in TOPMed is in [[https:// | ||
- | ======= | + | ======= |
- | ====== TOPMed ====== | + | While authorship is decided on an individual basis for each GSCAN paper, typically, authorship is arranged in groups. We hope the GIANT investigators will forgive us for adopting their authorship guidelines. |
- | Preliminary phenotype definitions for distributed analyses | + | * A group of 6 or fewer junior investigators who strongly led the efforts, usually starred to denote equal contribution, |
- | + | * In alphabetical order, junior investigators who had substantial individual contributions but not as much as those in Group 1. Typically, these might be lead analysts or other junior investigators who made a sizable contribution such as GWA analyses performed specifically for the paper. | |
- | The list of dbGaP studies | + | |
+ | | ||
+ | * In alphabetical order, senior investigators who had contributions worthy of authorship and contributed more than those in group 4. Typically, these might be a lead PI of a participating cohort who did not participate as strongly in GSCAN activities as those in group 6. | ||
+ | * In alphabetical order, senior investigators who participated strongly | ||
+ | * The senior investigators who strongly led/oversaw the writing and/or analysis of the paper, including a subset that are co-corresponding authors (usually 6 or fewer). | ||