Summary Statistics

Linear files (.linear files) store summary statistics from a linear model. We follow the PLINK2 .glm.linear file format and use the following columns.

Name	Type	Description
CHROM	string	The name of the chromosome to which this SNP belongs (ex: 1)
POS	integer	The position of this SNP on the chromosome (ex: 10114)
ID	string	A unique identifier for this SNP in the file (ex: ‘rs1234’)
P	float	The p-value assigned to this SNP via association testing (ex: 43.078)

Examples

See tests/data/test_snpstats.linear for an example of a short .linear file:

#CHROM  POS     ID      REF     ALT     A1      TEST    OBS_CT  BETA    SE      T_STAT  P       ERRCODE
1       10114   1:10114:T:C     T       C       C       ADD     2504    -0.010774       1.0004  -0.09   0.99    .
1       10116   1:10116:A:G     A       G       A       ADD     2504    -0.436  1.00034 -0.345  0.2345  .
1       10117   1:10117:C:A     C       A       A       ADD     2504    1.50    0.45    2.5     0.0005  .
1       10122   1:10122:A:G     A       G       A       ADD     2504    1.00    0.001   42.0    1.26e-102       .