Reserved headers
Here is a list of all headers (gl.Sumstats.data) used in GWASLab functions. These headers are fixed to avoid ambiguity within GWASLab framework.
| Header | Datatype | Description | Note |
|---|---|---|---|
SNPID |
string |
variant ID (CHR:POS:NEA:EA) | GWASLab assumes EA=ALT and NEA=REF |
rsID |
string |
dbSNP rsID | - |
CHR |
Int64 |
chromosome number (X 23, Y 24, MT 25) | - |
POS |
Int64 |
base pair position | - |
EA |
category |
effect allele | - |
NEA |
category |
non-effect allele | - |
STATUS |
category |
variant standardization & harmonization status | - |
REF |
category |
reference allele in reference genome | - |
ALT |
category |
alternative allele | - |
EAF |
float64 |
effect allele frequency | - |
NEAF |
float64 |
non-effect allele frequency | - |
MAF |
float64 |
minor allele frequency | - |
INFO |
float32 |
imputation INFO/RSQ | - |
BETA |
float64 |
effect size beta | - |
SE |
float64 |
standard error of beta | - |
BETA_95U |
float64 |
upper bound of beta 95% condidence interval | - |
BETA_95L |
float64 |
lower bound of beta 95% condidence interval | - |
OR |
float64 |
odds ratio | - |
OR_95U |
float64 |
upper bound of OR 95% condidence interval | - |
OR_95L |
float64 |
lower bound of OR 95% condidence interval | - |
HR |
float64 |
hazard ratio | - |
HR_95U |
float64 |
upper bound of HR 95% condidence interval | - |
HR_95L |
float64 |
lower bound of HR 95% condidence interval | - |
CHISQ |
float64 |
chi square | - |
Z |
float64 |
z score | - |
T |
float64 |
t statistics | - |
F |
float64 |
F statistics | - |
P |
float64 |
P value | - |
P_MANTISSA |
float64 |
P mantissa | - |
P_EXPONENT |
float64 |
P exponent | - |
MLOG10P |
float64 |
\(-log_{10}(P)\) | - |
SNPR2 |
float64 |
per variant R2 | - |
DOF |
Int64 |
degree of freedom | - |
P_HET |
float64 |
heterogeneity test P value | - |
I2_HET |
float64 |
heterogeneity I2 | - |
DENSITY |
Int64 |
signal density | - |
N |
Int64 |
total sample size | - |
N_CASE |
Int64 |
number of cases | - |
N_CONTROL |
Int64 |
number of controls | - |
GENENAME |
string |
nearest gene symbol | - |
CIS/TRANS |
string |
whether the variant is in cis or trans region | Cis,Trans,NoReference |
DISTANCE_TO_KNOWN |
Int64 |
distance to nearest known variants | - |
LOCATION_OF_KNOWN |
string |
relative location to nearest known variants | Same,Upstream,Downstream,NoReference |
KNOWN_ID |
string |
nearest known variant ID | - |
KNOWN_PUBMED_ID |
string |
pubmed ID of the known variant | - |
KNOWN_AUTHOR |
string |
author of the study | - |
KNOWN_SET_VARIANT |
string |
known set and overlapping variant | - |
KNOWN_VARIANT |
string |
known variant overlapping with the variant | - |
KNOWN_SET |
string |
variant set of the known variant | - |
NOVEL |
string |
if the identified variants are novel | - |