Skip to content

fix website build #480

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
danielnachun merged 1 commit into from
Apr 22, 2026
Merged

fix website build #480

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion .github/recipe/recipe.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@ requirements:
- ${{ stdlib('c') }}
- ${{ compiler('cxx') }}
host:
- bioconductor-biostrings
- bioconductor-iranges
- bioconductor-qvalue
- bioconductor-s4vectors
Expand Down
1 change: 0 additions & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@ Authors@R: c(person("Gao Wang",role = c("cre","aut"),
person("StatFunGen Lab", role = "ctb"))
License: MIT + file LICENSE
Imports:
Biostrings,
GenomicRanges,
IRanges,
MungeSumstats,
Expand Down
2 changes: 1 addition & 1 deletion R/allele_qc.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ match_ref_panel <- function(target_data, ref_variants, col_to_flip = NULL,
remove_indels = FALSE, remove_strand_ambiguous = TRUE,
flip_strand = FALSE, remove_unmatched = TRUE, ...) {
strand_flip <- function(ref) {
as.character(Biostrings::reverseComplement(Biostrings::DNAStringSet(ref)))
chartr("ATCG", "TAGC", ref)
}

# helper to sanitize column names to avoid NA/empty names that break dplyr verbs
Expand Down
1 change: 0 additions & 1 deletion pixi.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ r45 = {features = ["r45"]}
"r-rcmdcheck" = "*"
"r-testthat" = "*"
"r-tidyverse" = "*"
"bioconductor-biostrings" = "*"
"bioconductor-iranges" = "*"
"bioconductor-qvalue" = "*"
"bioconductor-s4vectors" = "*"
Expand Down
5 changes: 4 additions & 1 deletion vignettes/dentist.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,9 @@ Here we demonstrate count mode on the full dataset, which avoids the "<2000 vari
First, we load the genotype data and align alleles between the summary statistics and the reference panel.

```{r prepare-data}
# Compute z-scores from beta/se
sumstat$z <- sumstat$beta / sumstat$se

# Load reference panel variant info
bim <- as.data.frame(vroom(paste0(bfile, ".bim"),
col_names = c("chrom", "variant_id", "gd", "pos", "A1", "A2"),
Expand Down Expand Up @@ -99,7 +102,7 @@ ref_df <- data.frame(
qc_result <- allele_qc(
target_data = target_df, ref_variants = ref_df,
col_to_flip = "z", match_min_prop = 0,
remove_dups = TRUE, remove_strand_ambiguous = TRUE
remove_dups = TRUE, remove_indels = TRUE, remove_strand_ambiguous = TRUE
)
aligned <- qc_result$target_data_qced
aligned <- aligned[order(aligned$pos), ]
Expand Down