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I am using SeqSQC and could get results for MissingRate, SexCheck and Inbreeding
However while trying to run IBD and PCA didnot work, it says could not find function
> seqfile<-PCA(seqfile, remove.samples=NULL)
Error in PCA(seqfile, remove.samples = NULL) :
could not find function "PCA"
> seqfile <- IBD(seqfile, remove.samples=NULL)
Error in IBD(seqfile, remove.samples = NULL) :
could not find function "IBD"
> sessionInfo( )
R version 4.3.0 (2023-04-21)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS/LAPACK: /cluster/users/thomasti/anaconda3/envs/r_4.3.0/lib/libopenblasp-r0.3.23.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Zurich
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeqSQC_1.22.0 SNPRelate_1.34.1 gdsfmt_1.36.1
[4] ExperimentHub_2.8.1 AnnotationHub_3.8.0 BiocFileCache_2.8.0
[7] dbplyr_2.3.3 BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7
[3] rlang_1.1.1 magrittr_2.0.3
[5] e1071_1.7-13 compiler_4.3.0
[7] RSQLite_2.3.1 png_0.1-8
[9] vctrs_0.6.3 maps_3.4.1
[11] reshape2_1.4.4 stringr_1.5.0
[13] httpcode_0.3.0 pkgconfig_2.0.3
[15] crayon_1.5.2 fastmap_1.1.1
[17] XVector_0.40.0 ellipsis_0.3.2
[19] labeling_0.4.3 utf8_1.2.3
[21] promises_1.2.1 rmarkdown_2.25
[23] bit_4.0.5 xfun_0.40
[25] zlibbioc_1.46.0 cachem_1.0.8
[27] GenomeInfoDb_1.36.3 jsonlite_1.8.7
[29] blob_1.2.4 gistr_0.9.0
[31] later_1.3.1 reshape_0.8.9
[33] interactiveDisplayBase_1.38.0 pryr_0.1.6
[35] R6_2.5.1 bslib_0.5.1
[37] stringi_1.7.12 RColorBrewer_1.1-3
[39] GGally_2.1.2 GenomicRanges_1.52.0
[41] jquerylib_0.1.4 Rcpp_1.0.11
[43] assertthat_0.2.1 knitr_1.44
[45] IRanges_2.34.1 httpuv_1.6.11
[47] tidyselect_1.2.0 yaml_2.3.7
[49] codetools_0.2-19 curl_5.0.2
[51] lattice_0.21-8 tibble_3.2.1
[53] plyr_1.8.8 Biobase_2.60.0
[55] shiny_1.7.5 withr_2.5.0
[57] KEGGREST_1.40.0 evaluate_0.21
[59] proxy_0.4-27 Biostrings_2.68.1
[61] pillar_1.9.0 BiocManager_1.30.22
[63] filelock_1.0.2 stats4_4.3.0
[65] generics_0.1.3 RCurl_1.98-1.12
[67] BiocVersion_3.17.1 S4Vectors_0.38.2
[69] ggplot2_3.4.3 munsell_0.5.0
[71] scales_1.2.1 xtable_1.8-4
[73] class_7.3-22 glue_1.6.2
[75] lazyeval_0.2.2 tools_4.3.0
[77] hexbin_1.28.3 grid_4.3.0
[79] rbokeh_0.5.2 AnnotationDbi_1.62.2
[81] colorspace_2.1-0 GenomeInfoDbData_1.2.10
[83] cli_3.6.1 rappdirs_0.3.3
[85] fansi_1.0.4 dplyr_1.1.3
[87] gtable_0.3.4 sass_0.4.7
[89] digest_0.6.33 crul_1.4.0
[91] htmlwidgets_1.6.2 farver_2.1.1
[93] memoise_2.0.1 htmltools_0.5.6
[95] lifecycle_1.0.3 httr_1.4.7
[97] mime_0.12 bit64_4.0.5
Thank you, it worked when I gave
IBDCheck
andPCACheck
The vignette here https://www.bioconductor.org/packages/devel/bioc/vignettes/SeqSQC/inst/doc/vignette.html had the syntax as
IBD
andPCA
.