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drop sample argument #300

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merged 1 commit into from
Oct 29, 2023
Merged

drop sample argument #300

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29 changes: 21 additions & 8 deletions R/methods.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3927,11 +3927,17 @@ setGeneric("test_gene_rank", function(.data,

}

# DEPRECATION OF reference function
if (is_present(.sample) & !is.null(.sample)) {

# Signal the deprecation to the user
deprecate_warn("1.13.2", "tidybulk::test_gene_rank(.sample = )", details = "The argument .sample is now deprecated and not needed anymore.")

}

# Get column names
.sample = enquo(.sample)
.sample = get_sample(.data, .sample)$.sample
.arrange_desc = enquo(.arrange_desc)
.entrez = enquo(.entrez)
.arrange_desc = enquo(.arrange_desc)
.entrez = enquo(.entrez)

# Check if ranking is set
if(quo_is_missing(.arrange_desc))
Expand All @@ -3955,19 +3961,26 @@ setGeneric("test_gene_rank", function(.data,
# Check if missing entrez
if(.data |> filter(is.na(!!.entrez)) |> nrow() > 0 ){
warning("tidybulk says: there are .entrez that are NA. Those will be removed")
.data = .data |> filter(!!.entrez |> is.na() |> not())
.data = .data |> filter(is.na(!!.entrez) |> not())
}

# Check if missing .arrange_desc
if(.data |> filter(is.na(!!.arrange_desc)) |> nrow() > 0 ){
warning("tidybulk says: there are .arrange_desc that are NA. Those will be removed")
.data = .data |> filter(!!.arrange_desc |> is.na() |> not())
.data = .data |> filter(is.na(!!.arrange_desc ) |> not())
}

.data |>
pivot_transcript(!!.entrez) |>
arrange(desc(!!.arrange_desc)) |>
select(!!.entrez, !!.arrange_desc) |>
distinct() |>

# Select one entrez - NEEDED?
with_groups(c(!!.entrez,!!.arrange_desc ), slice, 1) |>

# arrange
arrange(desc(!!.arrange_desc)) |>

# Format
deframe() |>
entrez_rank_to_gsea(species, gene_collections = gene_sets ) |>

Expand Down