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