add support for LD matrix and use better genotype readers

.github/recipe/recipe.yaml

@@ -24,17 +24,21 @@ requirements:
     - ${{ compiler('cxx') }}
   host:
     - bioconductor-biocparallel
+    - bioconductor-biocsingular
+    - bioconductor-gdsarray
     - bioconductor-genomicranges
     - bioconductor-iranges
     - bioconductor-qvalue
     - bioconductor-s4vectors
     - bioconductor-snprelate
     - bioconductor-snpstats
-    - bioconductor-mungesumstats
     - bioconductor-multiassayexperiment
+    - bioconductor-plinkmatrix
     - bioconductor-rsamtools
     - bioconductor-rtracklayer
+    - bioconductor-seqarray
     - bioconductor-summarizedexperiment
+    - bioconductor-variantannotation
     - r-archive
     - r-arrow
     - r-aspu
@@ -49,6 +53,7 @@ requirements:
     - r-cpp11
     - r-cpp11armadillo
     - r-ctwas
+    - r-dbi
     - r-dplyr
     - r-flashier
     - r-fsusier
@@ -79,6 +84,7 @@ requirements:
     - r-rfast
     - r-rlang
     - r-robustbase
+    - r-rsqlite
     - r-softimpute
     - r-stringr
     - r-susier
@@ -92,17 +98,21 @@ requirements:
     - r-yaml
   run:
     - bioconductor-biocparallel
+    - bioconductor-biocsingular
+    - bioconductor-gdsarray
     - bioconductor-genomicranges
     - bioconductor-iranges
     - bioconductor-qvalue
     - bioconductor-s4vectors
     - bioconductor-snprelate
     - bioconductor-snpstats
     - bioconductor-multiassayexperiment
-    - bioconductor-mungesumstats
+    - bioconductor-plinkmatrix
     - bioconductor-rsamtools
     - bioconductor-rtracklayer
+    - bioconductor-seqarray
     - bioconductor-summarizedexperiment
+    - bioconductor-variantannotation
     - r-archive
     - r-arrow
     - r-aspu
@@ -117,6 +127,7 @@ requirements:
     - r-cpp11
     - r-cpp11armadillo
     - r-ctwas
+    - r-dbi
     - r-dplyr
     - r-flashier
     - r-fsusier
@@ -147,6 +158,7 @@ requirements:
     - r-rfast
     - r-rlang
     - r-robustbase
+    - r-rsqlite
     - r-softimpute
     - r-stringr
     - r-susier

DESCRIPTION

@@ -72,22 +72,26 @@ Suggests:
     coda,
     CorShrink,
     ctwas,
+    DBI,
     ebnm,
     flashier,
     fsusieR,
     GBJ,
+    GDSArray,
     gdsfmt,
     glmnet,
     harmonicmeanp,
     igraph,
     knitr,
     L0Learn,
+    logging,
     mashr,
     mr.mashr,
     mvsusieR,
     ncvreg,
     nnls,
     pgenlibr,
+    PlinkMatrix,
     plinkQC,
     plyranges,
     poolr,
@@ -97,7 +101,9 @@ Suggests:
     Rfast,
     rmarkdown,
     robustbase,
+    RSQLite,
     rtracklayer,
+    SeqArray,
     SNPRelate,
     snpStats,
     testthat,
@@ -119,6 +125,8 @@ VignetteBuilder: knitr
 Config/roxygen2/version: 8.1.0
 Collate:
     'AllGenerics.R'
+    'GenotypeMixture.R'
+    'LdMatrix.R'
     'RangedTupleList.R'
     'GenotypeHandle.R'
     'AllClasses.R'
@@ -128,24 +136,24 @@ Collate:
     'tupleSelectors.R'
     'CtwasResult.R'
     'CtwasResultEntry.R'
+    'GenotypeDosageSeed.R'
     'GwasFineMappingResult.R'
+    'MethodOptions.R'
+    'MethodParam.R'
     'H2Estimate.R'
     'JointGroup.R'
     'LdBlocks.R'
-    'LdData.R'
     'LdStatistic.R'
     'LdEigen.R'
     'LdScore.R'
     'MashPrior.R'
-    'MethodOptions.R'
-    'MethodParam.R'
+    'qtlSumStats.R'
     'QtlDataset.R'
     'MultiStudyQtlDataset.R'
     'QtlFineMappingResult.R'
     'SldscData.R'
     'causalInferencePipeline.R'
     'gwasSumStats.R'
-    'qtlSumStats.R'
     'fineMappingPipeline.R'
     'ld.R'
     'colocPipeline.R'