UW-GAC dbgaptools issues

UW-GAC / dbgaptools

R package to create and check standard files for dbGaP submission

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issues

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Feature/fix failing build

#41 amstilp closed 3 years ago
0
feature/df-args

#40 broomej opened 4 years ago
0
adding "good" dd to check_sattr() and check_pheno() causes testing error

#39 broomej opened 4 years ago
6
Feature/read processed files

#38 amstilp opened 4 years ago
0
Fix devtools::check notes about LICENSE

#37 amstilp opened 4 years ago
0
write a vignette

#36 smgogarten opened 4 years ago
0
make output more user-friendly

#35 smgogarten opened 4 years ago
2
tailor check functions to current submission guide

#34 smgogarten opened 4 years ago
3
write_dbgap takes output directory argument

#33 smgogarten opened 4 years ago
0
add verbose flag to control printing

#32 smgogarten opened 4 years ago
0
make helper functions for repeated tasks

#31 smgogarten opened 4 years ago
0
accept data frames as function arguments

#30 smgogarten opened 4 years ago
1
ped_consent_err should account for phenotypes

#29 smgogarten opened 4 years ago
0
export .check_dd()

#28 broomej opened 4 years ago
0
Add helpful message to .check_dd() when DD entries don't match DS variable names

#27 broomej opened 5 years ago
0
fix encoded value check for mixed type variables

#26 smgogarten closed 5 years ago
1
Allow for multiple phenotype files in check_cross_file

#25 emeryl opened 5 years ago
0
improve checking of consent codes

#24 laurieca opened 5 years ago
1
don't check for SAMPLE_USE

#23 laurieca closed 5 years ago
1
add check for consistency between pedigree and phenotype sex

#22 smgogarten opened 5 years ago
0
Feature/cleanup hidden files

#21 amstilp closed 5 years ago
0
Add checks for illegal chars in IDs

#20 sarahcn opened 5 years ago
0
Import %>% function

#19 amstilp closed 5 years ago
2
allow xml DD input

#18 sarahcn closed 4 years ago
2
Add subject consent file check for check where only one of SUBJECT_SOURCE or SOURCE_SUBJECT_ID is populated

#17 sarahcn opened 6 years ago
0
change read* functions to external (vs internal)

#16 sarahcn closed 6 years ago
0
add checks for unconsented singletons

#15 sarahcn opened 6 years ago
0
Consider returning ds and dd from check functions

#14 sarahcn opened 6 years ago
1
allow for .xls(x) DS input

#13 sarahcn opened 6 years ago
3
check for duplicated IDs

#12 smgogarten closed 5 years ago
3
variables with multiple DD types

#11 sarahcn opened 6 years ago
0
error if DD VARNAME does not match DS

#10 smgogarten opened 6 years ago
3
read_dd_file fails for DD with no "VALUES" column

#9 smgogarten closed 6 years ago
5
Revise MIN and MAX checks in check_dd

#8 sarahcn opened 6 years ago
2
Allow Excel (.xls or .xlsx) input DS with warning, rather than exiting with error

#7 sarahcn closed 5 years ago
1
Revise .check_dd to deal with a variable named "NA"

#6 sarahcn opened 6 years ago
0
Revise names of error reports returned by check* functions

#5 sarahcn opened 6 years ago
0
Fix check_ped for blank MZ twin column

#4 sarahcn opened 6 years ago
0
Fix .read_dd_file for multiple blank column names

#3 sarahcn closed 6 years ago
1
Add capability to parse processed DD and DS

#2 sarahcn opened 6 years ago
4
Remove code_devel

#1 sarahcn closed 6 years ago
1