Add data-raw/XFORCE.R (no dataset yet)

data-raw/XFORCE.R

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+library(tidyverse)
+library(biomaRt)
+
+xraw = readxl::read_xlsx("data-raw/FORCE-data.xlsx",
+                         skip = 2,
+                         n_max = 5422,  # skip bad ones at the bottom
+                         col_types = "text")
+
+x = xraw |>
+  dplyr::filter(startsWith(Type, "XSNP")) |>
+  dplyr::select(CHROM = Chromosome, MARKER = SNP, POS = "GRCh38 Region",
+         REF = "Reference Allele", ALT = "Alternate Allele") |>
+  dplyr::mutate(POS = as.integer(POS)) |>
+  print()
+
+# NB: Doesn't work with version 111
+mart = useEnsembl(biomart = "snps", dataset = "hsapiens_snp", version = 110)
+info = getBM(
+  attributes = c("refsnp_id", "chr_name", "chrom_start", "minor_allele", "minor_allele_freq", "minor_allele_count"),
+  filters = c("snp_filter"),
+  values = list(x$MARKER),
+  mart = mart
+) |> as_tibble() |> print()
+
+filter(info, minor_allele == "")
+anyDuplicated(info$refsnp_id)
+
+y = left_join(x, info, by = c(MARKER = "refsnp_id")) |>
+  dplyr::filter(minor_allele != "") |>
+  dplyr::mutate(
+    MB = POS / 1e6,
+    A1 = if_else(minor_allele == REF, ALT, REF),
+    A2 = if_else(minor_allele == REF, REF, ALT),
+    FREQ1 = 1 - minor_allele_freq
+  ) # |> print
+
+# Checks
+filter(y, POS != chrom_start)
+filter(y, is.na(FREQ1))
+filter(y, nchar(A1) !=1 | nchar(A2) !=1)
+
+# Final table
+XFORCE = y |>
+  dplyr::select(CHROM, MARKER, MB, A1, A2, FREQ1) |>
+  as.data.frame()
+
+print(head(XFORCE))
+save
+# usethis::use_data(FORCE, overwrite = TRUE)