Error of the transcription factor foot printing
When using Footprint function, the error message had shown as below.
Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, :
attempt to extract more than one element
When using other gene, such as GATA2, I can run Footprint function.
Therefore, I guess the environment is probably correct.
In particular, setting of motif.name = c("MEIS2") may be the problem because there are 2-MEIS2 motifs according to JASPAR2022.
Are any solutions for this problem?
Thank you for your kindness.
signac.obj <- Footprint(
+ object = signac.obj,
+ motif.name = c("MEIS2"),
+ genome = BSgenome.Mmusculus.UCSC.mm10
+ )
Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, :
attempt to extract more than one element
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.4.2 Signac_1.7.0 sp_1.5-0 SeuratObject_4.1.2
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.2 usethis_2.1.6 devtools_2.4.5 GenomeInfoDb_1.30.1 tools_4.1.1
[7] profvis_0.3.7 utf8_1.2.2 rgdal_1.5-32 R6_2.5.1 irlba_2.3.5.1 rgeos_0.5-9
[13] DBI_1.1.3 BiocGenerics_0.40.0 colorspace_2.0-3 urlchecker_1.0.1 tidyselect_1.2.0 prettyunits_1.1.1
[19] processx_3.7.0 curl_4.3.3 compiler_4.1.1 progressr_0.11.0 cli_3.4.1 scales_1.2.1
[25] callr_3.7.2 pbapply_1.5-0 stringr_1.4.1 digest_0.6.29 Rsamtools_2.10.0 XVector_0.34.0
[31] pkgconfig_2.0.3 htmltools_0.5.3 parallelly_1.32.1 sessioninfo_1.2.2 fastmap_1.1.0 htmlwidgets_1.5.4
[37] rlang_1.0.6 rstudioapi_0.14 shiny_1.7.2 generics_0.1.3 BiocParallel_1.28.3 dplyr_1.0.10
[43] RCurl_1.98-1.9 magrittr_2.0.3 GenomeInfoDbData_1.2.7 patchwork_1.1.2 Matrix_1.5-1 Rcpp_1.0.9
[49] munsell_0.5.0 S4Vectors_0.32.4 fansi_1.0.3 lifecycle_1.0.3 stringi_1.7.8 zlibbioc_1.40.0
[55] pkgbuild_1.3.1 grid_4.1.1 parallel_4.1.1 listenv_0.8.0 promises_1.2.0.1 crayon_1.5.2
[61] miniUI_0.1.1.1 lattice_0.20-45 Biostrings_2.62.0 ps_1.7.1 pillar_1.8.1 GenomicRanges_1.46.1
[67] future.apply_1.9.1 codetools_0.2-18 stats4_4.1.1 pkgload_1.3.0 fastmatch_1.1-3 glue_1.6.2
[73] data.table_1.14.4 vctrs_0.4.2 httpuv_1.6.6 gtable_0.3.1 purrr_0.3.5 tidyr_1.2.1
[79] future_1.28.0 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.6 mime_0.12 xtable_1.8-4
[85] later_1.3.0 RcppRoll_0.3.0 tibble_3.1.8 memoise_2.0.1 IRanges_2.28.0 globals_0.16.1
[91] ellipsis_0.3.2
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