Output Formats
Reference for all output file formats produced by Binx.
GWAS Results
Output from binx gwas:
| Column | Type | Description |
|---|---|---|
marker_id | string | Marker identifier |
chrom | string | Chromosome |
pos | integer | Base pair position |
model | string | Genetic model used |
score | float | -log10(p-value) |
p_value | float | Association p-value |
effect | float | Effect size estimate |
n_obs | integer | Sample size (non-missing) |
threshold | float | Significance threshold used |
Kinship Matrix
Output from binx kinship:
- Tab-separated values
- Square symmetric matrix
- Sample IDs as header and first column
- Values represent genetic relatedness (typically 0-2)
QTL Results
Output from binx qtl:
| Column | Type | Description |
|---|---|---|
marker_id | string | Peak marker |
chrom | string | Chromosome |
pos | integer | Position |
model | string | Best model |
score | float | -log10(p-value) |
effect | float | Effect size |
threshold | float | Significance threshold used |
Plot Outputs
binx plot supports:
.svg- Scalable Vector Graphics (recommended for publication).png- PNG raster image