expand and improve RSS TWAS functions

.Rbuildignore

@@ -13,3 +13,4 @@
 ^dev$
 ^air.toml
 ^inst/prototype
+^LICENSE$

.github/environment/pixi.toml

@@ -14,7 +14,7 @@ codecov = "cd $GITHUB_WORKSPACE; R -e 'covr::codecov(quiet = FALSE)'"
 rcmdcheck = "cd $GITHUB_WORKSPACE; R -e 'rcmdcheck::rcmdcheck(error_on = \"error\", args = c(\"--no-manual\", \"--no-build-vignettes\"))'"
 bioccheck_git_clone = "cd $GITHUB_WORKSPACE; R -e 'BiocCheck::BiocCheckGitClone(\"quit-with-status\" = TRUE)'"
 bioccheck = "cd $GITHUB_WORKSPACE; R -e 'BiocCheck::BiocCheck(\"quit-with-status\" = FALSE)'"
-goodpractice = "cd $GITHUB_WORKSPACE; R -e 'goodpractice::gp(\".\")'"
+goodpractice = "cd $GITHUB_WORKSPACE; R -e 'goodpractice::gp(\".\", checks = stringr::str_subset(goodpractice::all_checks(), \"^(covr|rcmdcheck_)\", negate = TRUE))'"
 use_major_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"major\", push = FALSE)'"
 use_minor_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"minor\", push = FALSE)'"
 use_patch_version = "cd $GITHUB_WORKSPACE; R -e 'usethis::use_version(which = \"patch\", push = FALSE)'"

.github/recipe/recipe.yaml

@@ -55,12 +55,14 @@ requirements:
     - r-ctwas
     - r-dbi
     - r-dplyr
+    - r-fdrtool
     - r-flashier
     - r-fsusier
     - r-gbj
     - r-glmnet
     - r-glue
     - r-harmonicmeanp
+    - r-hibayes
     - r-igraph
     - r-l0learn
     - r-magrittr
@@ -129,12 +131,14 @@ requirements:
     - r-ctwas
     - r-dbi
     - r-dplyr
+    - r-fdrtool
     - r-flashier
     - r-fsusier
     - r-gbj
     - r-glmnet
     - r-glue
     - r-harmonicmeanp
+    - r-hibayes
     - r-igraph
     - r-l0learn
     - r-magrittr
@@ -176,7 +180,7 @@ tests:
       - R -e "library('pecotmr')"
 
 about:
-  license: MIT
+  license: GPL-3.0-only
   license_file: LICENSE
   summary: pecotmr implements pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate QTL and GWAS analysis based on a fine-mapped single effects model.
   homepage: https://github.com/StatFunGen/pecotmr

DESCRIPTION

@@ -2,7 +2,6 @@ Encoding: UTF-8
 Type: Package
 Package: pecotmr
 Version: 0.9.4
-Date: 2026-02-28
 Title: Post-GWAS 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.
 URL: https://statfungen.github.io/pecotmr, https://github.com/StatFunGen/pecotmr
@@ -12,7 +11,8 @@ Authors@R: c(person("Gao Wang",role = c("cre","aut"),
                   person("Daniel Nachun", role = "aut",
                   email = "dnachun@stanford.edu"),
                   person("StatFunGen Lab", role = "ctb"))
-License: MIT + file LICENSE
+License: GPL-3
+Copyright: See the file inst/COPYRIGHTS for code included from other projects.
 biocViews:
     StatisticalMethod,
     GenomeWideAssociation,
@@ -51,6 +51,7 @@ Imports:
     Rsamtools,
     S4Arrays,
     S4Vectors,
+    SparseArray,
     stringr,
     SummarizedExperiment,
     susieR (>= 0.16.4),
@@ -74,13 +75,15 @@ Suggests:
     ctwas,
     DBI,
     ebnm,
+    fdrtool,
     flashier,
     fsusieR,
     GBJ,
     GDSArray,
     gdsfmt,
     glmnet,
     harmonicmeanp,
+    hibayes,
     igraph,
     knitr,
     L0Learn,
@@ -138,15 +141,15 @@ Collate:
     'CtwasResult.R'
     'GenotypeDosageSeed.R'
     'GwasFineMappingResult.R'
-    'MethodOptions.R'
-    'MethodParam.R'
     'H2Estimate.R'
     'JointGroup.R'
     'LdBlocks.R'
     'LdStatistic.R'
     'LdEigen.R'
     'LdScore.R'
     'MashPrior.R'
+    'MethodOptions.R'
+    'MethodParam.R'
     'qtlSumStats.R'
     'QtlDataset.R'
     'MultiStudyQtlDataset.R'