iCNV_detection(snp_lrr=snp_lrr, snp_baf = snp_baf,
snp_lrr.pos = snp_lrr.pos,snp_baf.pos = snp_baf.pos,
projname="projectname",CN=1,mu=c(-3,0,2),cap=TRUE,visual = 2)
'cnv' is not recognized as an internal or external command,
operable program or batch file.
command works if using example with ngs data from vignette.
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] iCNV_0.99.27 CODEX_1.22.0 BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.58.0
[5] rtracklayer_1.49.5 Rsamtools_2.6.0 Biostrings_2.58.0 XVector_0.30.0
[9] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2 IRanges_2.24.1 S4Vectors_0.28.1
[13] BiocGenerics_0.36.0 magrittr_2.0.1 readr_1.4.0 devtools_2.3.2
[17] usethis_2.0.0
loaded via a namespace (and not attached):
[1] lattice_0.20-41 prettyunits_1.1.1 ps_1.5.0 assertthat_0.2.1 rprojroot_2.0.2
[6] digest_0.6.27 R6_2.5.0 evaluate_0.14 pillar_1.4.7 zlibbioc_1.36.0
[11] rlang_0.4.10 curl_4.3 rstudioapi_0.13 callr_3.5.1 Matrix_1.2-18
[16] rmarkdown_2.6 desc_1.2.0 BiocParallel_1.24.1 stringr_1.4.0 RCurl_1.98-1.2
[21] DelayedArray_0.16.0 compiler_4.0.3 xfun_0.20 pkgconfig_2.0.3 pkgbuild_1.2.0
[26] htmltools_0.5.0 SummarizedExperiment_1.20.0 tibble_3.0.5 GenomeInfoDbData_1.2.4 matrixStats_0.57.0
[31] XML_3.99-0.5 fansi_0.4.2 crayon_1.3.4 withr_2.4.0 GenomicAlignments_1.26.0
[36] bitops_1.0-6 grid_4.0.3 jsonlite_1.7.2 lifecycle_0.2.0 stringi_1.5.3
[41] cli_2.2.0 fs_1.5.0 remotes_2.2.0 testthat_3.0.1 ellipsis_0.3.1
[46] vctrs_0.3.6 tools_4.0.3 Biobase_2.50.0 glue_1.4.2 purrr_0.3.4
[51] hms_1.0.0 MatrixGenerics_1.2.0 yaml_2.2.1 processx_3.4.5 pkgload_1.1.0
[56] sessioninfo_1.1.1 memoise_1.1.0 knitr_1.30