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update data.table syntax to avoid triggering CRAN check NOTE #72

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Merged
alkaZeltser merged 3 commits into from
Mar 4, 2025
Merged

update data.table syntax to avoid triggering CRAN check NOTE #72

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7251812
update data.table syntax to avoid triggering CRAN check NOTE
alkaZeltser Feb 26, 2025
5e3db84
add walrus operator to data.table imports
alkaZeltser Feb 27, 2025
2374cb8
lintr fixes
alkaZeltser Feb 27, 2025
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3 changes: 2 additions & 1 deletion NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@ import('vcfR');
importFrom(
'data.table',
'tstrsplit',
'setDT'
'setDT',
':='
);
import('reshape2');
import('BoutrosLab.plotting.general');
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5 changes: 3 additions & 2 deletions R/combine-vcf-with-pgs.R
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@@ -1,3 +1,4 @@
utils::globalVariables(c('ID', 'new.ID', '.')); # data table syntax work-around for CRAN legitimacy
#' @title Combine VCF with PGS
#' @description Match PGS SNPs to corresponding VCF information by genomic coordinates or rsID using a merge operation.
#' @param vcf.data A data.frame containing VCF data. Required columns: \code{CHROM, POS}.
Expand Down Expand Up @@ -111,8 +112,8 @@ combine.vcf.with.pgs <- function(vcf.data, pgs.weight.data) {
split.rsid.vcf.data <- merge(
x = vcf.data,
# split only entries with multiple rsIDs, save in new column, and merge back with the original data
y = vcf.data[grepl(';', ID), unique(unlist(strsplit(as.character(ID), ';', fixed = TRUE))), by = .(Indiv, CHROM, POS)
][,.(new.ID = V1, Indiv, CHROM, POS)],
y = vcf.data[grepl(';', get('ID')), unique(unlist(strsplit(as.character(get('ID')), ';', fixed = TRUE))), by = .(get('Indiv'), get('CHROM'), get('POS'))
][,.(new.ID = get('V1'), get('Indiv'), get('CHROM'), get('POS'))],
by = c('CHROM', 'POS', 'Indiv'),
all = TRUE
);
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