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preset: Filter reference genes and add warnings

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This commit is contained in:
Elias Projahn 2022-01-17 20:22:50 +01:00
parent 53f955f3da
commit ab61f08d0d
1 changed files with 25 additions and 1 deletions
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26
R/preset.R
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@ -35,11 +35,35 @@ preset <- function(reference_gene_ids,
gene gene
] ]
reference_gene_ids_excluded <- reference_gene_ids[
!reference_gene_ids %chin% gene_ids_filtered
]
if (length(reference_gene_ids_excluded > 0)) {
warning(paste0(
"The following reference gene IDs are excluded from the preset ",
"because they don't have enough data: ",
paste(reference_gene_ids_excluded, collapse = ", ")
))
}
reference_gene_ids_included <- reference_gene_ids[
reference_gene_ids %chin% gene_ids_filtered
]
if (length(reference_gene_ids_included) < 1) {
stop(paste0(
"There has to be at least one reference gene for the preset to be ",
"valid. Please note that some methods may require more reference ",
"genes."
))
}
# The included data gets sorted to be able to produce predictable hashes # The included data gets sorted to be able to produce predictable hashes
# for the object later. # for the object later.
structure( structure(
list( list(
reference_gene_ids = sort(reference_gene_ids), reference_gene_ids = sort(reference_gene_ids_included),
methods = methods, methods = methods,
species_ids = sort(species_ids), species_ids = sort(species_ids),
gene_ids = sort(gene_ids_filtered) gene_ids = sort(gene_ids_filtered)