fchen365 / surf Goto Github PK

Hi,

I get an error when parsing the events from the annotation. I tested using the same input as you did, but I still get this error.
Here is my code:

library(rtracklayer)
library(usethis)
library(surf)

anno_file <- "/Data/gencode.v32.primary_assembly.annotation.gtf"
anno_hs <- import(anno_file)
gene_id <- anno_hs[seqnames(anno_hs) == "chr16" &
anno_hs$gene_type == "protein_coding" &
anno_hs$type == "gene"]$gene_id
gene_id_sampled <- sample(unique(gene_id), 24)
anno_hs_select <- anno_hs[anno_hs$gene_id %in% gene_id_sampled]

export(anno_hs_select, "/Data/gencode.v32.primary.example.gtf")

event <- parseEvent("/Data/gencode.v32.primary.example.gtf")

Error in initialize(value, ...) :
'initialize' method returned an object of class “DFrame” instead of the required class “surf”

The issue seems to come from

res <- new("surf",
anno_event,
genePartsList = genePartsList,
sampleData = DataFrameList())

in the annotateEvent() function.

Thank you in advance for your help.

Best,

Joao Lourenco

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] usethis_2.1.6 rtracklayer_1.56.1 surf_0.99.1 DEXSeq_1.42.0 RColorBrewer_1.1-3
[6] AnnotationDbi_1.58.0 DESeq2_1.36.0 SummarizedExperiment_1.26.1 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
[11] IRanges_2.30.1 S4Vectors_0.34.0 MatrixGenerics_1.8.1 matrixStats_0.62.0 Biobase_2.56.0
[16] BiocGenerics_0.42.0 BiocParallel_1.30.3 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2

loaded via a namespace (and not attached):
[1] fs_1.5.2 bitops_1.0-7 bit64_4.0.5 filelock_1.0.2 progress_1.2.2
[6] httr_1.4.4 tools_4.2.0 doRNG_1.8.2 utf8_1.2.2 R6_2.5.1
[11] DBI_1.1.3 colorspace_2.0-3 tidyselect_1.1.2 prettyunits_1.1.1 bit_4.0.4
[16] curl_4.3.2 compiler_4.2.0 cli_3.4.1 xml2_1.3.3 DelayedArray_0.22.0
[21] scales_1.2.1 genefilter_1.78.0 rappdirs_0.3.3 stringr_1.4.1 digest_0.6.29
[26] Rsamtools_2.12.0 XVector_0.36.0 pkgconfig_2.0.3 dbplyr_2.2.1 fastmap_1.1.0
[31] rlang_1.0.6 rstudioapi_0.14 RSQLite_2.2.18 BiocIO_1.6.0 generics_0.1.3
[36] hwriter_1.3.2.1 dplyr_1.0.10 RCurl_1.98-1.9 magrittr_2.0.3 GenomeInfoDbData_1.2.8
[41] Matrix_1.5-1 Rcpp_1.0.9 munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.2
[46] yaml_2.3.5 stringi_1.7.8 zlibbioc_1.42.0 BiocFileCache_2.4.0 grid_4.2.0
[51] blob_1.2.3 crayon_1.5.2 lattice_0.20-45 Biostrings_2.64.1 splines_4.2.0
[56] annotate_1.74.0 hms_1.1.2 KEGGREST_1.36.3 locfit_1.5-9.6 knitr_1.40
[61] pillar_1.8.1 rjson_0.2.21 rngtools_1.5.2 geneplotter_1.74.0 codetools_0.2-18
[66] biomaRt_2.52.0 XML_3.99-0.11 glue_1.6.2 png_0.1-7 vctrs_0.4.2
[71] gtable_0.3.1 purrr_0.3.4 tidyr_1.2.1 assertthat_0.2.1 cachem_1.0.6
[76] ggplot2_3.3.6 xfun_0.33 xtable_1.8-4 restfulr_0.0.15 survival_3.3-1
[81] tibble_3.1.8 GenomicAlignments_1.32.1 memoise_2.0.1 statmod_1.4.37 ellipsis_0.3.2