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Statistical-Genetics
jass_preprocessing
Commits
3a03bac4
Commit
3a03bac4
authored
Jan 04, 2021
by
Hanna JULIENNE
Browse files
fix filer on imputation quality
parent
b0380f32
Pipeline
#44528
passed with stages
in 1 minute and 22 seconds
Changes
2
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1
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doc/source/index.rst
View file @
3a03bac4
...
...
@@ -97,11 +97,11 @@ Input
Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
Some fields are optional like the imputation_quality. If not used they can be filled with na.
.. csv-table:: GWAS information table!
:header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
"GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na
:header: "filename","consortia","outcome","fullName","type","Nsample","Ncase","Ncontrol","Nsnp","snpid","a1","a2","freq","pval","n","z","OR","se","code","imp","ncas","ncont"
,"imputation_quality"
"GIANT_HEIGHT_Wood_et_al.txt","GIANT","HEIGHT","Height","Anthropometry",253288, na, na, 2550858, "MarkerName", "Allele1", "Allele2", "Freq.Allele1.HapMapCEU","p","N","b",na,"SE",na,na,na,na
, "imputationInfo"
Command line usage example:
...
...
jass_preprocessing/map_gwas.py
View file @
3a03bac4
...
...
@@ -169,7 +169,7 @@ def read_gwas( gwas_internal_link, column_map, imputation_treshold=None):
print
(
fullGWAS
.
head
())
if
imputation_treshold
:
fullGWAS
=
fullGWAS
.
loc
[
full
Name
.
imputation_quality
>
imputation_treshold
]
fullGWAS
=
fullGWAS
.
loc
[
full
GWAS
.
imputation_quality
>
imputation_treshold
]
fullGWAS
=
fullGWAS
[
~
fullGWAS
.
index
.
duplicated
(
keep
=
'first'
)]
#fullGWAS = convert_missing_values(fullGWAS)
...
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