Hi

Trying to run VariantFilter, manage to import fine,

PED file is pretty standard:

FAM001 SAMPLE_C SAMPLE_P1 SAMPLE_P2 1 2

FAM001 SAMPLE_P1 0 0 0 1

FAM001 SAMPLE_P2 0 0 0 1

> vfpar

VariantFiltering parameter object

  VCF file(s): merged_PASS.vcf.bgz
  Genome version(s): NA(UCSC)
  Number of individuals: 3 (SAMPLE_C, SAMPLE_P1, SAMPLE_P2)
  PED file: trio.ped
  Genome-centric annotation package: BSgenome.Hsapiens.UCSC.hg38 (UCSC hg38)
  Variant-centric annotation package: SNPlocs.Hsapiens.dbSNP144.GRCh38 (dbSNP dbSNP Human BUILD 144)
  Transcript-centric annotation package: TxDb.Hsapiens.UCSC.hg38.knownGene
  Gene-centric annotation package: org.Hs.eg.db
  Radical/Conservative AA changes: AA_chemical_properties_HanadaGojoboriLi2006.tsv
  Codon usage table: humanCodonUsage.txt
  Regions to annotate: CodingVariants, IntronVariants, FiveSpliceSiteVariants, ThreeSpliceSiteVariants, PromoterVariants, FiveUTRVariants, ThreeUTRVariants
  Other annotation pkg/obj: MafDb.1Kgenomes.phase1.GRCh38,
                            PolyPhen.Hsapiens.dbSNP131,
                            SIFT.Hsapiens.dbSNP137,
                            phastCons100way.UCSC.hg38,
                            humanGenesPhylostrata
  All transcripts: FALSE

> reHo<-autosomalRecessiveHomozygous(vfpar)
Error in `$<-.data.frame`(`*tmp*`, "Phenotype", value = 0) : 
  replacement has 1 row, data has 0

>sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] phastCons100way.UCSC.hg38_3.7.1          SIFT.Hsapiens.dbSNP137_1.0.0            
 [3] PolyPhen.Hsapiens.dbSNP131_1.0.2         RSQLite_2.2.14                          
 [5] MafDb.1Kgenomes.phase1.GRCh38_3.10.0     GenomicScores_2.6.1                     
 [7] SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20 TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0
 [9] GenomicFeatures_1.46.5                   org.Hs.eg.db_3.14.0                     
[11] AnnotationDbi_1.56.2                     BSgenome.Hsapiens.UCSC.hg38_1.4.4       
[13] BSgenome_1.62.0                          rtracklayer_1.54.0                      
[15] VariantFiltering_1.30.0                  VariantAnnotation_1.40.0                
[17] Rsamtools_2.10.0                         Biostrings_2.62.0                       
[19] XVector_0.34.0                           SummarizedExperiment_1.24.0             
[21] Biobase_2.54.0                           GenomicRanges_1.46.1                    
[23] GenomeInfoDb_1.30.1                      IRanges_2.28.0                          
[25] S4Vectors_0.32.4                         MatrixGenerics_1.6.0                    
[27] matrixStats_0.62.0                       BiocGenerics_0.40.0                     

loaded via a namespace (and not attached):
  [1] backports_1.4.1               Hmisc_4.7-2                   AnnotationHub_3.2.2          
  [4] BiocFileCache_2.2.1           lazyeval_0.2.2                splines_4.1.0                
  [7] BiocParallel_1.28.3           ggplot2_3.3.6                 digest_0.6.29                
 [10] ensembldb_2.18.4              htmltools_0.5.2               fansi_1.0.3                  
 [13] magrittr_2.0.3                checkmate_2.1.0               memoise_2.0.1                
 [16] cluster_2.1.2                 annotate_1.72.0               prettyunits_1.1.1            
 [19] jpeg_0.1-9                    colorspace_2.0-3              blob_1.2.3                   
 [22] rappdirs_0.3.3                xfun_0.31                     dplyr_1.0.9                  
 [25] jsonlite_1.8.0                crayon_1.5.1                  RCurl_1.98-1.7               
 [28] graph_1.72.0                  genefilter_1.76.0             shinyTree_0.2.7              
 [31] survival_3.2-11               glue_1.6.2                    gtable_0.3.0                 
 [34] zlibbioc_1.40.0               DelayedArray_0.20.0           Rhdf5lib_1.16.0              
 [37] HDF5Array_1.22.1              scales_1.2.0                  DBI_1.1.3                    
 [40] Rcpp_1.0.8.3                  xtable_1.8-4                  progress_1.2.2               
 [43] htmlTable_2.4.1               foreign_0.8-81                bit_4.0.4                    
 [46] Formula_1.2-4                 DT_0.28                       htmlwidgets_1.5.4            
 [49] httr_1.4.3                    RColorBrewer_1.1-3            ellipsis_0.3.2               
 [52] pkgconfig_2.0.3               XML_3.99-0.10                 Gviz_1.38.4                  
 [55] nnet_7.3-16                   dbplyr_2.2.1                  deldir_1.0-6                 
 [58] locfit_1.5-9.7                utf8_1.2.2                    tidyselect_1.1.2             
 [61] rlang_1.0.6                   later_1.3.0                   munsell_0.5.0                
 [64] BiocVersion_3.14.0            tools_4.1.0                   cachem_1.0.6                 
 [67] cli_3.3.0                     generics_0.1.3                stringr_1.4.0                
 [70] fastmap_1.1.0                 yaml_2.3.5                    knitr_1.39                   
 [73] bit64_4.0.5                   purrr_0.3.4                   KEGGREST_1.34.0              
 [76] AnnotationFilter_1.18.0       RBGL_1.70.0                   mime_0.12                    
 [79] xml2_1.3.3                    biomaRt_2.50.3                shinythemes_1.2.0            
 [82] compiler_4.1.0                rstudioapi_0.13               filelock_1.0.2               
 [85] curl_4.3.2                    png_0.1-7                     interactiveDisplayBase_1.32.0
 [88] tibble_3.1.7                  geneplotter_1.72.0            stringi_1.7.6                
 [91] lattice_0.20-44               ProtGenerics_1.26.0           Matrix_1.3-3                 
 [94] shinyjs_2.1.0                 vctrs_0.4.1                   pillar_1.7.0                 
 [97] lifecycle_1.0.1               rhdf5filters_1.6.0            BiocManager_1.30.18          
[100] data.table_1.14.2             bitops_1.0-7                  httpuv_1.6.5                 
[103] R6_2.5.1                      BiocIO_1.4.0                  latticeExtra_0.6-30          
[106] promises_1.2.0.1              gridExtra_2.3                 dichromat_2.0-0.1            
[109] assertthat_0.2.1              rhdf5_2.38.1                  DESeq2_1.34.0                
[112] rjson_0.2.21                  GenomicAlignments_1.30.0      GenomeInfoDbData_1.2.7       
[115] parallel_4.1.0                hms_1.1.1                     grid_4.1.0                   
[118] rpart_4.1.16                  biovizBase_1.42.0             shiny_1.7.1                  
[121] base64enc_0.1-3               tinytex_0.40                  interp_1.1-3                 
[124] restfulr_0.0.15

Dear Andrew,

Thanks for your bug reporting. This has been fixed in the devel and release versions of VariantFiltering, concretely release version 1.36.1, which will become available in the next 24/48 hours via BiocManager::install("VariantFiltering"). Note that you are using an outdated version of R (4.1.0, current one is 4.3.1) and consequenctly an outdated version of the Bioconductor packages too, including VariantFiltering 1.30.0, which cannot be fixed as they have been archived.

To use the corrected version of VariantFiltereing you need to update your R and Bioconductor installations to the latest release, please follow the instructions at https://bioconductor.org/install.