SeqSQC R library, functions PCA and IBD not working
1
0
Entering edit mode
ttom ▴ 10
@7ad41a40
Last seen 6 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 • 389 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 32 minutes 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?

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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