Semi-automatically check all deprecated args in a given function.
check_deprecated(
fun = "finemap_loci",
pkg = "echolocatoR",
when = "2.0.0",
args = match.call(),
lifecycle_fun = lifecycle::deprecate_warn,
reassign = FALSE,
map = list(A1_col = "colmap", A2_col = "colmap", chrom_col = "colmap", position_col =
"colmap", effect_col = "colmap", freq_col = "colmap", gene_col = "colmap", locus_col
= "colmap", MAF_col = "colmap", N_cases = "colmap", N_controls = "colmap",
N_cases_col = "colmap", N_controls_col = "colmap", sample_size = "colmap", MAF_col =
"colmap", pval_col = "colmap", stderr_col = "colmap", tstat_col = "colmap", snp_col =
"colmap", file_sep = NULL, probe_path = NULL, chrom_type = NULL, PAINTOR_QTL_datasets
= NULL,
QTL_prefixes = "qtl_suffixes", proportion_cases = NULL, server = NULL,
vcf_folder = NULL, top_SNPs = "topSNPs", PP_threshold = "credset_thresh",
consensus_threshold = "consensus_thresh", plot.types = "plot_types", plot.Roadmap =
"roadmap", plot.Roadmap_query = "roadmap_query", plot.XGR_libnames = "xgr_libnames",
plot.zoom = "zoom", plot.zoom = "zoom", plot.Nott_epigenome = "nott_epigenome",
plot.Nott_show_placseq = "nott_show_placseq")
)Function to check.
Package that the function is from.
A string giving the version when the behaviour was deprecated.
Argument calls to assess.
Which lifecycle function to use by default.
Attempt to reassign deprecated variables to the corresponding new variable (if applicable).
Mapping between old:new argument names. Use NULL
if the argument is no longer used at all.
topSNPs <- echodata::topSNPs_Nalls2019
fullSS_path <- echodata::example_fullSS()
#> Writing file to ==> /tmp/Rtmp0dbVNr/nalls2019.fullSS_subset.tsv
testthat::expect_error(
echolocatoR::finemap_loci(
fullSS_path = fullSS_path,
topSNPs = topSNPs,
loci = c("BST1","MEX3C"),
chrom_col = "CHR",
position_col = "BP")
)
#> Warning: Found 2 deprecated arguments used in: "CHR"