selecting biotypes for creating gene activity

[SinghalDivya]

Hi,

I am trying to create the gene activity matrix for not only protein-coding regions but also other mentioned biotypes such as biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"). But whenever i try to change the biotypes, i get following error:

> gene.activities <- GeneActivity(
+   pbmc,
+   assay = NULL,
+   features = NULL,
+   extend.upstream = 2000,
+   extend.downstream = 0,
+   biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
+   max.width = 5e+05,
+   gene.id = FALSE,
+   verbose = TRUE
+ )
Extracting gene coordinates
Error in FeatureMatrix(fragments = Fragments(object = object[[assay]]),  : 
  unused arguments (biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"), max.width = 5e+05, gene.id = FALSE)

It would be great if you could suggest to me how to include other biotypes.

Thank you

[timoast]

Can you show the output of sessionInfo()?

[SinghalDivya]

Hi Tim,

Thank you for your prompt response.
here is the output for sessionInfo()

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.4 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /work/gallo_lab/divya/softwares/miniconda3/envs/signac/lib/libopenblasp-r0.3.12.so

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

locale:
[1] C

attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] stringr_1.4.0 chromVAR_1.12.0
[3] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0
[5] rtracklayer_1.50.0 Biostrings_2.58.0
[7] XVector_0.30.0 EnsDb.Hsapiens.v86_2.99.0
[9] ensembldb_2.14.0 AnnotationFilter_1.14.0
[11] GenomicFeatures_1.42.2 AnnotationDbi_1.52.0
[13] TFBSTools_1.28.0 JASPAR2020_0.99.10
[15] cicero_1.3.4.11 Gviz_1.34.1
[17] monocle3_0.2.3.0 SingleCellExperiment_1.12.0
[19] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.1
[21] matrixStats_0.58.0 Biobase_2.50.0
[23] patchwork_1.1.1 ggplot2_3.3.5
[25] SeuratWrappers_0.3.0 future_1.21.0
[27] GenomicRanges_1.42.0 GenomeInfoDb_1.26.4
[29] IRanges_2.24.1 S4Vectors_0.28.1
[31] BiocGenerics_0.36.0 SeuratObject_4.0.0
[33] Seurat_4.0.1 Signac_1.1.1.9006

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0
[3] scattermore_0.7 GGally_2.1.1
[5] R.methodsS3_1.8.1 tidyr_1.1.3
[7] bit64_4.0.5 knitr_1.31
[9] R.utils_2.10.1 irlba_2.3.3
[11] DelayedArray_0.16.2 data.table_1.14.0
[13] rpart_4.1-15 KEGGREST_1.30.1
[15] RCurl_1.98-1.2 generics_0.1.0
[17] cowplot_1.1.1 RSQLite_2.2.4
[19] RANN_2.6.1 VGAM_1.1-5
[21] bit_4.0.4 spatstat.data_2.1-0
[23] xml2_1.3.2 httpuv_1.5.5
[25] assertthat_0.2.1 DirichletMultinomial_1.32.0
[27] viridis_0.5.1 xfun_0.24
[29] hms_1.0.0 promises_1.2.0.1
[31] fansi_0.5.0 progress_1.2.2
[33] caTools_1.18.1 dbplyr_2.1.1
[35] igraph_1.2.6 DBI_1.1.1
[37] htmlwidgets_1.5.3 reshape_0.8.8
[39] spatstat.geom_1.65-5 purrr_0.3.4
[41] ellipsis_0.3.2 dplyr_1.0.5
[43] backports_1.2.1 annotate_1.68.0
[45] biomaRt_2.46.3 deldir_0.2-10
[47] vctrs_0.3.8 remotes_2.2.0
[49] ROCR_1.0-11 abind_1.4-5
[51] cachem_1.0.4 withr_2.4.2
[53] ggforce_0.3.3 checkmate_2.0.0
[55] sctransform_0.3.2 GenomicAlignments_1.26.0
[57] prettyunits_1.1.1 goftest_1.2-2
[59] cluster_2.1.1 lazyeval_0.2.2
[61] seqLogo_1.56.0 crayon_1.4.1
[63] hdf5r_1.3.3 pkgconfig_2.0.3
[65] tweenr_1.0.1 nlme_3.1-152
[67] ProtGenerics_1.22.0 nnet_7.3-15
[69] rlang_0.4.11 globals_0.14.0
[71] lifecycle_1.0.0 miniUI_0.1.1.1
[73] BiocFileCache_1.14.0 rsvd_1.0.3
[75] dichromat_2.0-0 polyclip_1.10-0
[77] lmtest_0.9-38 graph_1.68.0
[79] Matrix_1.3-2 ggseqlogo_0.1
[81] zoo_1.8-9 base64enc_0.1-3
[83] ggridges_0.5.3 png_0.1-7
[85] viridisLite_0.4.0 bitops_1.0-7
[87] R.oo_1.24.0 KernSmooth_2.23-18
[89] blob_1.2.1 parallelly_1.24.0
[91] readr_1.4.0 jpeg_0.1-8.1
[93] CNEr_1.26.0 scales_1.1.1
[95] memoise_2.0.0 magrittr_2.0.1
[97] plyr_1.8.6 ica_1.0-2
[99] zlibbioc_1.36.0 compiler_4.0.3
[101] RColorBrewer_1.1-2 fitdistrplus_1.1-3
[103] Rsamtools_2.6.0 listenv_0.8.0
[105] pbapply_1.4-3 htmlTable_2.1.0
[107] Formula_1.2-4 MASS_7.3-53.1
[109] mgcv_1.8-34 tidyselect_1.1.0
[111] stringi_1.5.3 askpass_1.1
[113] latticeExtra_0.6-29 ggrepel_0.9.1
[115] VariantAnnotation_1.36.0 fastmatch_1.1-0
[117] tools_4.0.3 future.apply_1.7.0
[119] rstudioapi_0.13 TFMPvalue_0.0.8
[121] foreign_0.8-81 lsa_0.73.2
[123] gridExtra_2.3 farver_2.1.0
[125] Rtsne_0.15 digest_0.6.27
[127] BiocManager_1.30.16 shiny_1.6.0
[129] pracma_2.3.3 Rcpp_1.0.6
[131] later_1.1.0.1 RcppAnnoy_0.0.18
[133] OrganismDbi_1.32.0 httr_1.4.2
[135] ggbio_1.38.0 biovizBase_1.38.0
[137] colorspace_2.0-2 XML_3.99-0.6
[139] tensor_1.5 reticulate_1.18
[141] splines_4.0.3 uwot_0.1.10
[143] RBGL_1.66.0 RcppRoll_0.3.0
[145] spatstat.utils_2.1-0 plotly_4.9.3
[147] xtable_1.8-4 jsonlite_1.7.2
[149] poweRlaw_0.70.6 R6_2.5.0
[151] Hmisc_4.5-0 pillar_1.6.2
[153] htmltools_0.5.1.1 mime_0.10
[155] DT_0.17 glue_1.4.2
[157] fastmap_1.1.0 BiocParallel_1.24.1
[159] codetools_0.2-18 utf8_1.2.2
[161] lattice_0.20-41 spatstat.sparse_2.0-0
[163] tibble_3.1.3 curl_4.3
[165] leiden_0.3.7 gtools_3.8.2
[167] GO.db_3.12.1 openssl_1.4.3
[169] survival_3.2-10 munsell_0.5.0
[171] GenomeInfoDbData_1.2.4 reshape2_1.4.4
[173] gtable_0.3.0 spatstat.core_1.65-5

[timoast]

Can you try updating to the latest version of Signac?

[SinghalDivya]

As suggested, I updated the signac, still getting the same error.

gene.activities <- GeneActivity(

• pbmc,
• assay = NULL,
• features = NULL,
• extend.upstream = 2000,
• extend.downstream = 0,
• biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"),
• max.width = 5e+05,
• gene.id = FALSE,
• verbose = TRUE
• )
  Extracting gene coordinates
  Error in FeatureMatrix(fragments = Fragments(object = object[[assay]]), :
  unused arguments (biotypes = c("protein_coding", "lincRNA", "rRNA", "processed_transcript"), max.width = 5e+05, gene.id = FALSE)

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.4 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /work/gallo_lab/divya/softwares/miniconda3/envs/signac/lib/libopenblasp-r0.3.12.so

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

locale:
[1] C

attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base

other attached packages:
[1] stringr_1.4.0 chromVAR_1.12.0
[3] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0
[5] rtracklayer_1.50.0 Biostrings_2.58.0
[7] XVector_0.30.0 EnsDb.Hsapiens.v86_2.99.0
[9] ensembldb_2.14.0 AnnotationFilter_1.14.0
[11] GenomicFeatures_1.42.2 AnnotationDbi_1.52.0
[13] TFBSTools_1.28.0 JASPAR2020_0.99.10
[15] cicero_1.3.4.11 Gviz_1.34.1
[17] monocle3_0.2.3.0 SingleCellExperiment_1.12.0
[19] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.1
[21] matrixStats_0.58.0 Biobase_2.50.0
[23] patchwork_1.1.1 ggplot2_3.3.5
[25] SeuratWrappers_0.3.0 future_1.21.0
[27] GenomicRanges_1.42.0 GenomeInfoDb_1.26.4
[29] IRanges_2.24.1 S4Vectors_0.28.1
[31] BiocGenerics_0.36.0 SeuratObject_4.0.4
[33] Seurat_4.1.0 Signac_1.6.0

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0
[3] scattermore_0.7 GGally_2.1.1
[5] R.methodsS3_1.8.1 tidyr_1.1.3
[7] bit64_4.0.5 knitr_1.31
[9] R.utils_2.10.1 irlba_2.3.3
[11] DelayedArray_0.16.2 data.table_1.14.0
[13] rpart_4.1-15 KEGGREST_1.30.1
[15] RCurl_1.98-1.2 generics_0.1.0
[17] cowplot_1.1.1 RSQLite_2.2.4
[19] RANN_2.6.1 VGAM_1.1-5
[21] bit_4.0.4 spatstat.data_2.1-0
[23] xml2_1.3.2 httpuv_1.5.5
[25] assertthat_0.2.1 DirichletMultinomial_1.32.0
[27] viridis_0.5.1 xfun_0.24
[29] hms_1.0.0 promises_1.2.0.1
[31] fansi_0.5.0 progress_1.2.2
[33] caTools_1.18.1 dbplyr_2.1.1
[35] igraph_1.2.6 DBI_1.1.1
[37] htmlwidgets_1.5.3 reshape_0.8.8
[39] spatstat.geom_1.65-5 purrr_0.3.4
[41] ellipsis_0.3.2 dplyr_1.0.5
[43] backports_1.2.1 annotate_1.68.0
[45] biomaRt_2.46.3 deldir_0.2-10
[47] vctrs_0.3.8 remotes_2.2.0
[49] ROCR_1.0-11 abind_1.4-5
[51] cachem_1.0.4 withr_2.4.2
[53] ggforce_0.3.3 checkmate_2.0.0
[55] sctransform_0.3.3 GenomicAlignments_1.26.0
[57] prettyunits_1.1.1 goftest_1.2-2
[59] cluster_2.1.1 lazyeval_0.2.2
[61] seqLogo_1.56.0 crayon_1.4.1
[63] hdf5r_1.3.3 pkgconfig_2.0.3
[65] tweenr_1.0.1 nlme_3.1-152
[67] ProtGenerics_1.22.0 nnet_7.3-15
[69] rlang_0.4.11 globals_0.14.0
[71] lifecycle_1.0.0 miniUI_0.1.1.1
[73] BiocFileCache_1.14.0 rsvd_1.0.3
[75] dichromat_2.0-0 polyclip_1.10-0
[77] lmtest_0.9-38 graph_1.68.0
[79] Matrix_1.4-1 ggseqlogo_0.1
[81] zoo_1.8-9 base64enc_0.1-3
[83] ggridges_0.5.3 png_0.1-7
[85] viridisLite_0.4.0 bitops_1.0-7
[87] R.oo_1.24.0 KernSmooth_2.23-18
[89] blob_1.2.1 parallelly_1.24.0
[91] readr_1.4.0 jpeg_0.1-8.1
[93] CNEr_1.26.0 scales_1.1.1
[95] memoise_2.0.0 magrittr_2.0.1
[97] plyr_1.8.6 ica_1.0-2
[99] zlibbioc_1.36.0 compiler_4.0.3
[101] RColorBrewer_1.1-2 fitdistrplus_1.1-3
[103] Rsamtools_2.6.0 listenv_0.8.0
[105] pbapply_1.4-3 htmlTable_2.1.0
[107] Formula_1.2-4 MASS_7.3-53.1
[109] mgcv_1.8-34 tidyselect_1.1.0
[111] stringi_1.5.3 askpass_1.1
[113] latticeExtra_0.6-29 ggrepel_0.9.1
[115] VariantAnnotation_1.36.0 fastmatch_1.1-0
[117] tools_4.0.3 future.apply_1.7.0
[119] rstudioapi_0.13 TFMPvalue_0.0.8
[121] foreign_0.8-81 lsa_0.73.2
[123] gridExtra_2.3 farver_2.1.0
[125] Rtsne_0.15 digest_0.6.27
[127] BiocManager_1.30.16 shiny_1.6.0
[129] pracma_2.3.3 Rcpp_1.0.8.3
[131] later_1.1.0.1 RcppAnnoy_0.0.18
[133] OrganismDbi_1.32.0 httr_1.4.2
[135] ggbio_1.38.0 biovizBase_1.38.0
[137] colorspace_2.0-2 XML_3.99-0.6
[139] tensor_1.5 reticulate_1.18
[141] splines_4.0.3 uwot_0.1.10
[143] RBGL_1.66.0 RcppRoll_0.3.0
[145] spatstat.utils_2.1-0 plotly_4.9.3
[147] xtable_1.8-4 jsonlite_1.7.2
[149] poweRlaw_0.70.6 R6_2.5.0
[151] Hmisc_4.5-0 pillar_1.6.2
[153] htmltools_0.5.1.1 mime_0.10
[155] DT_0.17 glue_1.4.2
[157] fastmap_1.1.0 BiocParallel_1.24.1
[159] codetools_0.2-18 utf8_1.2.2
[161] lattice_0.20-41 spatstat.sparse_2.0-0
[163] tibble_3.1.3 curl_4.3
[165] leiden_0.3.7 gtools_3.8.2
[167] GO.db_3.12.1 openssl_1.4.3
[169] survival_3.2-10 munsell_0.5.0
[171] GenomeInfoDbData_1.2.4 reshape2_1.4.4
[173] gtable_0.3.0 spatstat.core_1.65-5

[timoast]

Should be fixed now on the develop branch

[SinghalDivya]

I am unable to install develop branch, is there something to do with R version?

remotes::install_github("timoast/signac", ref = "develop")
Downloading GitHub repo timoast/signac@develop
Skipping 6 packages not available: BiocGenerics, S4Vectors, Rsamtools, IRanges, GenomicRanges, GenomeInfoDb
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
5: Setting LC_PAPER failed, using "C"
6: Setting LC_MEASUREMENT failed, using "C"
v checking for file '/tmp/RtmpmGmuRG/remotes1cbbc615c25d76/timoast-signac-979cf4a/DESCRIPTION' ... OK

• preparing 'Signac':
  v checking DESCRIPTION meta-information ... OK
• cleaning src
• installing the package to process help pages
• saving partial Rd database (43.6s)
• cleaning src
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
  Removed empty directory 'Signac/.github'
  Removed empty directory 'Signac/vignettes'
• building 'Signac_1.6.0.9008.tar.gz'
  Warning: invalid uid value replaced by that for user 'nobody'
  Warning: invalid gid value replaced by that for user 'nobody'

Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted
Error: Failed to install 'Signac' from GitHub:
(converted from warning) installation of package '/tmp/RtmpmGmuRG/file1cbbc64cfbdb1c/Signac_1.6.0.9008.tar.gz' had non-zero exit status

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.4 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /work/gallo_lab/divya/softwares/miniconda3/envs/signac/lib/libopenblasp-r0.3.12.so

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] processx_3.5.2 compiler_4.0.3 R6_2.5.1 rprojroot_2.0.2
[5] cli_3.2.0 prettyunits_1.1.1 tools_4.0.3 withr_2.5.0
[9] curl_4.3.2 crayon_1.5.1 remotes_2.2.0 callr_3.7.0
[13] ps_1.6.0 pkgbuild_1.2.0

[timoast]

This looks like a locale issue unrelated to Signac, you could try some suggestions here: https://stackoverflow.com/questions/27299420/how-to-get-rid-of-warning-messages-after-installing-r