SeqSQC R library, functions PCA and IBD not working
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0
Entering edit mode
ttom ▴ 10
@7ad41a40
Last seen 13 months ago
Switzerland

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
SeqSQC • 602 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

There are no exported functions called PCA or IBD in the SeqSQC package. There are PCAcheck and IBDcheck, which might be what you are after?

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1
Entering edit mode

Thank you, it worked when I gave IBDCheck and PCACheck

The vignette here https://www.bioconductor.org/packages/devel/bioc/vignettes/SeqSQC/inst/doc/vignette.html had the syntax as IBD and PCA.

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