Fix namespace

cumc · Mar 10, 2024 · 4db90ef · 4db90ef
1 parent f80c196
commit 4db90ef
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Showing 5 changed files with 3 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Type: Package
 Package: pecotmr
-Version: 0.1.43
+Version: 0.1.44
 Date: 2024-03-09
 Title: Pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate molecular QTL and GWAS.
 Description: The majority of the statistical models in pecotmr are based on fine-mapped single effects described in Wang G et al (2020) JRSS-B. It also incorporates wrappers to a series of useful TWAS methods as well as utility functions for QTL and GWAS integration.

diff --git a/NAMESPACE b/NAMESPACE
@@ -64,7 +64,6 @@ import(susieR)
 import(tibble)
 import(tidyr)
 importFrom(GBJ,GBJ)
-importFrom(Rcpp,evalCpp)
 importFrom(Rfast,cora)
 importFrom(coloc,coloc.bf_bf)
 importFrom(data.table,as.data.table)
@@ -102,7 +101,6 @@ importFrom(mvsusieR,mvsusie)
 importFrom(pgenlibr,GetVariantCt)
 importFrom(pgenlibr,NewPgen)
 importFrom(pgenlibr,ReadList)
-importFrom(plink2R,read_plink)
 importFrom(purrr,compact)
 importFrom(purrr,map)
 importFrom(purrr,map2)

diff --git a/R/compute_qtl_enrichment.R b/R/compute_qtl_enrichment.R
@@ -53,7 +53,6 @@
 #' 
 #' @seealso \code{\link[susieR]{susie}}
 #' @useDynLib pecotmr
-#' @importFrom Rcpp evalCpp 
 #' @export
 #' 
 compute_qtl_enrichment <- function(gwas_pip, susie_qtl_regions, 
@@ -89,4 +88,4 @@ compute_qtl_enrichment <- function(gwas_pip, susie_qtl_regions,
  shrinkage_lambda = lambda,
  num_threads = num_threads)
  return(en)
-}
+}
diff --git a/R/file_utils.R b/R/file_utils.R
@@ -1,7 +1,5 @@
 # This needs pgenlibr package
 # devtools::install_github("chrchang/plink-ng", subdir="/2.0/pgenlibr")
-# and PLINK2R
-# Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE); remotes::install_github('gabraham/plink2R', subdir='plink2R', ref='d74be015e8f54d662b96c6c2a52a614746f9030d')
 
 # read PLINK files
 #' @importFrom dplyr rename

diff --git a/R/misc.R b/R/misc.R
@@ -68,7 +68,7 @@ format_variant_id <- function(names_vector) {
 
 load_genotype_data <- function(genotype, keep_indel = TRUE) {
  # Read genotype data using plink
- geno <- read_plink(genotype)
+ geno <- plink2R::read_plink(genotype)
  # Process row names
  rownames(geno$bed) <- sapply(strsplit(rownames(geno$bed), ":"), `[`, 2)
  # Remove indels if specified
@@ -337,7 +337,6 @@ add_Y_residuals <- function(data_list, conditions, scale_residuals = FALSE) {
  return(data_list)
 }
 
-#' @importFrom plink2R read_plink
 #' @import purrr dplyr tibble
 #' @importFrom utils read.table
 #' @importFrom tidyr unnest