```
# parati
**parati** is an R package for inferring maternal and paternal transmitted and
non-transmitted alleles from phased trio genotype data.
The package is designed for trio-based SNP-level analyses, including studies of
genetic nurture and transgenerational effects. It integrates with Bioconductor
workflows by supporting both VCF file paths and `VariantAnnotation::VCF`
objects as input.
---
## Features
- Trio-aware inference of transmitted and non-transmitted parental alleles
- Support for phased VCF genotype data
- Input as either:
- a VCF/VCF.GZ file path
- a `VariantAnnotation::VCF` object
- Returns R objects for downstream analysis rather than writing files by default
- Includes toy example data for testing and demonstration
---
## Installation
### Bioconductor
```r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("parati")
```
### Development version
```
# install.packages("remotes")
remotes::install_github("newche/parati")
```
------
## Input data
`parati` requires two inputs:
1. Trio genotype data in VCF format
2. A family index table describing family membership and roles
------
### 1. Trio genotype VCF
Supported input types:
- a path to a phased VCF/VCF.GZ file
- a `VariantAnnotation::VCF` object
Expected content:
- standard VCF fixed columns
- genotype columns whose sample IDs match the family table
- autosomal biallelic SNPs are recommended
Sample IDs in the VCF must exactly match the `IndividualID` column of the
family table.
---
#### Example VCF input
Below is a partial example from the simulated testing dataset
`Toy_TrioGenotype.vcf.gz`:
```text
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1-M 1-P 1-B 2-M 2-P 2-B
1 100000 rs1 G T . PASS . GT 0/0 0/1 0/1 0/0 0/1 0/1
1 101000 rs2 A C . PASS . GT 0/0 0/1 0/0 0/0 0/0 0/0
1 102000 rs3 A T . PASS . GT 0/0 0/0 0/0 1/1 1/1 0/1
1 103000 rs4 A G . PASS . GT 0/1 0/1 0/1 0/1 0/0 ./.
1 104000 rs5 A G . PASS . GT 0/1 0/0 0/1 0/0 0/1 0/0
1 105000 rs6 T C . PASS . GT 0/0 1/1 0/1 1/1 0/1 0/1
1 106000 rs7 T C . PASS . GT 0/0 0/0 0/0 0/1 0/0 0/1
1 107000 rs8 A C . PASS . GT 0/0 0/0 0/0 ./. 0/1 0/1
...
```
------
### 2. Family index table
The family table must contain the following columns:
| Column name | Description |
| ------------ | ---------------------------------------------------- |
| FamilyIndex | Family identifier |
| IndividualID | Sample identifier matching the VCF sample name |
| Role | Family role: `F` (father), `M` (mother), `C` (child) |
The family input can be provided as:
- a path to an `.xlsx` file
- a `data.frame`
- a `data.table`
---
#### Example family index
```text
FamilyIndex IndividualID Role
1 1-M M
1 1-P F
1 1-B C
2 2-M M
2 2-P F
2 2-B C
3 3-M M
3 3-P F
3 3-B C
...
```
---
------
## Example
```
library(parati)
vcf_file <- system.file("extdata", "Toy_TrioGenotype.vcf.gz", package = "parati")
fam_file <- system.file("extdata", "Toy_FamilyIndexTable.xlsx", package = "parati")
res <- parati_run(
vcf = vcf_file,
fam = fam_file,
chr = 1,
hap_length = 500000
)
names(res)
head(res$vcf_trans, 3)
head(res$vcf_nontrans, 3)
head(res$sim_perc_summary, 3)
```
------
## Integration with Bioconductor workflows
```
library(parati)
library(VariantAnnotation)
vcf_file <- system.file("extdata", "Toy_TrioGenotype.vcf.gz", package = "parati")
fam_file <- system.file("extdata", "Toy_FamilyIndexTable.xlsx", package = "parati")
vcf_obj <- readVcf(vcf_file, genome = "unknown")
res <- parati_run(
vcf = vcf_obj,
fam = fam_file,
chr = 1
)
```
------
## Output
`parati_run()` returns a named list containing:
- `vcf_trans`
- `vcf_nontrans`
- `sim_perc_summary`
These are returned as R objects for further analysis.
------
## Example data
Toy example data are included in:
```
inst/extdata/
```
Files:
- `Toy_TrioGenotype.vcf.gz`
- `Toy_FamilyIndexTable.xlsx`
------
## License
GPL-3 + file LICENSE
------
## Contact
For questions or issues, please open an issue on GitHub.
https://github.com/newche/parati/issues
