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Prepare PAINTOR annotations

Source: R/PAINTOR_prepare_annotations.R
PAINTOR_prepare_annotations.Rd

Convert BED annotation files into a PAINTOR-format annotation matrix. For each SNP in the locus file, checks whether its position falls within any interval in each BED file, producing a binary (0/1) matrix.

Usage

PAINTOR_prepare_annotations(
  BED_paths,
  dat_merged,
  PT_results_path,
  locus_dir,
  verbose = TRUE
)

Arguments

BED_paths

Character vector of paths to BED files (can be gzipped). Each BED file becomes one annotation column.

dat_merged

data.table with at least CHR and POS columns containing the SNPs to annotate.

PT_results_path

Directory where the annotation matrix will be written.

locus_dir

Locus directory (used for naming the output file).

verbose

Print messages.

Value

Path to the annotation matrix file.

Details

This is a pure-R reimplementation of the original AnnotateLocus.py Python 2.7 utility bundled with PAINTOR.