convert.pgs.to.bed {ApplyPolygenicScore} | R Documentation |
Convert PGS data to BED format
Description
Convert imported and formatted PGS compnent SNP coordinate data to BED format.
Usage
convert.pgs.to.bed(
pgs.weight.data,
chr.prefix = TRUE,
numeric.sex.chr = FALSE,
slop = 0
)
Arguments
pgs.weight.data |
A data.frame containing SNP coordinate data with standardized CHROM and POS columns. |
chr.prefix |
A logical indicating whether the 'chr' prefix should be used when formatting chromosome name. |
numeric.sex.chr |
A logical indicating whether the sex chromosomes should be formatted numerically, as opposed to alphabetically. |
slop |
An integer indicating the number of base pairs to add to the BED interval on either side. |
Value
A data.frame containing the PGS component SNP coordinate data in BED format and any other columns provided in pgs.weight.data.
Examples
pgs.weight.data <- data.frame(
CHROM = c('chr1', 'chrX'),
POS = c(10, 20)
);
convert.pgs.to.bed(pgs.weight.data);
# Switch between different chromosome notations
convert.pgs.to.bed(pgs.weight.data, chr.prefix = FALSE, numeric.sex.chr = TRUE);
# Add slop to BED intervals
convert.pgs.to.bed(pgs.weight.data, slop = 10);
[Package ApplyPolygenicScore version 3.0.1 Index]