Error in split.default(lis_obj, names(lis_obj)) :

[snashraf]

I have tried running scarHRD on my data.

scar_score("sequenza/0200135321.seqz.gz",reference = "grch37", seqz=TRUE)
Preprocessing started...
Collecting GC information ........... done

Error in split.default(lis_obj, names(lis_obj)) :
first argument must be a vector

Below is output of the sessionInfo()> sessionInfo()

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] scarHRD_0.1.0 devtools_2.3.0 usethis_1.6.1 forcats_0.5.0 purrr_0.3.4 readr_1.3.1
[7] tibble_3.0.1 tidyverse_1.3.0 cowplot_1.0.0 stringr_1.4.0 tidyr_1.1.0 data.table_1.12.8
[13] ComplexHeatmap_2.4.2 ggplot2_3.3.0 dplyr_0.8.5 GenVisR_1.20.0 maftools_2.4.0

loaded via a namespace (and not attached):
[1] colorspace_1.4-1 copynumber_1.15.0 rjson_0.2.20 ellipsis_0.3.1
[5] rprojroot_1.3-2 circlize_0.4.9 XVector_0.28.0 GenomicRanges_1.40.0
[9] GlobalOptions_0.1.1 fs_1.4.1 clue_0.3-57 rstudioapi_0.11
[13] remotes_2.1.1 bit64_0.9-7 AnnotationDbi_1.50.0 fansi_0.4.1
[17] lubridate_1.7.8 xml2_1.3.2 splines_4.0.0 pkgload_1.0.2
[21] jsonlite_1.6.1 Rsamtools_2.4.0 FField_0.1.0 broom_0.5.6
[25] cluster_2.1.0 dbplyr_1.4.4 png_0.1-7 BiocManager_1.30.10
[29] compiler_4.0.0 httr_1.4.1 backports_1.1.7 assertthat_0.2.1
[33] Matrix_1.2-18 cli_2.0.2 prettyunits_1.1.1 tools_4.0.0
[37] gtable_0.3.0 glue_1.4.1 GenomeInfoDbData_1.2.3 rappdirs_0.3.1
[41] Rcpp_1.0.4.6 Biobase_2.48.0 cellranger_1.1.0 vctrs_0.3.0
[45] Biostrings_2.56.0 nlme_3.1-147 rtracklayer_1.48.0 ps_1.3.3
[49] testthat_2.3.2 rvest_0.3.5 lifecycle_0.2.0 gtools_3.8.2
[53] XML_3.99-0.3 zlibbioc_1.34.0 scales_1.1.1 BSgenome_1.56.0
[57] VariantAnnotation_1.34.0 hms_0.5.3 parallel_4.0.0 SummarizedExperiment_1.18.1
[61] RColorBrewer_1.1-2 curl_4.3 pbapply_1.4-2 memoise_1.1.0
[65] gridExtra_2.3 biomaRt_2.44.0 stringi_1.4.6 RSQLite_2.2.0
[69] desc_1.2.0 S4Vectors_0.26.1 GenomicFeatures_1.40.0 BiocGenerics_0.34.0
[73] pkgbuild_1.0.8 BiocParallel_1.22.0 shape_1.4.4 GenomeInfoDb_1.24.0
[77] rlang_0.4.6 pkgconfig_2.0.3 matrixStats_0.56.0 bitops_1.0-6
[81] lattice_0.20-41 GenomicAlignments_1.24.0 processx_3.4.2 bit_1.1-15.2
[85] tidyselect_1.1.0 plyr_1.8.6 magrittr_1.5 R6_2.4.1
[89] IRanges_2.22.2 generics_0.0.2 squash_1.0.9 DelayedArray_0.14.0
[93] DBI_1.1.0 pillar_1.4.4 haven_2.3.0 withr_2.2.0
[97] survival_3.1-12 RCurl_1.98-1.2 seqminer_8.0 modelr_0.1.8
[101] crayon_1.3.4 utf8_1.1.4 sequenza_3.0.0 BiocFileCache_1.12.0
[105] viridis_0.5.1 GetoptLong_0.1.8 progress_1.2.2 readxl_1.3.1
[109] callr_3.4.3 blob_1.2.1 reprex_0.3.0 digest_0.6.25
[113] openssl_1.4.1 stats4_4.0.0 munsell_0.5.0 viridisLite_0.3.0
[117] iotools_0.3-1 sessioninfo_1.1.1 askpass_1.1

[snashraf]

Here is the first few lines of the data.

head(a)
chromosome position base.ref depth.normal depth.tumor depth.ratio Af Bf zygosity.normal GC.percent good.reads AB.normal AB.tumor
1 1 12817 N 3 20 7.626 1.000 0 hom 56 42 N .
2 1 12852 G 4 21 5.250 1.000 0 het 56 21 GA .
3 1 12856 C 4 22 5.500 0.955 0 hom 56 22 C T0.045
4 1 12868 N 7 24 3.377 1.000 0 hom 59 51 N .
5 1 12888 A 8 24 3.000 0.958 0 hom 59 24 A G0.042
6 1 12919 N 10 36 3.629 1.000 0 hom 60 51 N .
tumor.strand
1 0
2 0
3 T1.0
4 0
5 G1.0
6 0

[oghzzang]

I think this error resulted from "chromosome name"

If you edit "1" to "chr1", you can fix it.

[snashraf]

Thanks alot !! It works !!

…

On Tue, Jun 2, 2020 at 5:29 AM stellaoh ***@***.***> wrote: I think this error resulted from "chromosome name" If you edit "1" to "chr1", you can fix it. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBFIN3MMMETDP7TNDPEH53RURPY5ANCNFSM4NOV4O6Q> .

-- Syed Najeeb Ashraf

[squigzzz]

IT works for me tooo !!!

[nroak]

Yes, adding the option chr.in.names=F fixed this error.