getCounts error

[jf292]

Hi,

I am running into an error when using the getCounts function:
fragment_counts <- getCounts(singlecellbams, final_peaks, paired=TRUE, by_rg=FALSE, format = "bam", colData= data.frame(celltype = cellnames))

It seems to be an issue with the bam files rather than the peaks as I can get fragment_counts using the same peaks with a different set of bam files. Would you be able to shed some light on the issue?

Many thanks,
Julia

Error in validObject(.Object): invalid class “GRanges” object:
'x@strand' is not parallel to 'x'

Traceback:

1. getCounts(singlecellbams2, final_peaks, paired = TRUE, by_rg = FALSE,
   . format = "bam", colData = data.frame(celltype = cellnames))
2. get_counts_from_bams(alignment_files, peaks, paired, by_rg, colData)
3. bamToFragments(bams[i], paired = paired)
4. GRanges(seqnames = scanned$rname, IRanges(start = scanned$pos,
   . width = 1), strand = "+")
5. new_GRanges("GRanges", seqnames = seqnames, ranges = ranges,
   . strand = strand, mcols = mcols, seqlengths = seqlengths,
   . seqinfo = seqinfo)
6. new(Class, seqnames = seqnames, ranges = ranges, strand = strand,
   . elementMetadata = mcols, seqinfo = seqinfo)
7. initialize(value, ...)
8. initialize(value, ...)
9. validObject(.Object)
10. stop(msg, ": ", errors, domain = NA)

[janemd2012]

I have a similar issue with getCounts with my own data and testing example(https://rdrr.io/bioc/chromVAR/man/getCounts.html). error message is the same(: I have no clue how to fix it and would appreciate very much if anyone help me fix it. Many thanks in advance!

code used:

`

First we'll read in some peaks

peaks_file <- system.file("extdata", "test_bed.txt", package = "chromVAR")
test_peaks <- getPeaks(peaks_file, sort = TRUE)

With single bam with RG tags (can also give multiple bams with RG)

test_rg <- system.file("extdata", "test_RG.bam", package = "chromVAR")
test_counts <- getCounts(test_rg, peaks = test_peaks, by_rg = TRUE,
paired = TRUE,
colData = S4Vectors::DataFrame(condition ="A"))
`

error message

Error in getCounts(test_rg, peaks = test_peaks, by_rg = TRUE, paired = TRUE, :
unused arguments (peaks = test_peaks, by_rg = TRUE, paired = TRUE, colData = S4Vectors::DataFrame(condition = "A"))

session info

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2020.2.254/linux/mkl/lib/intel64_lin/libmkl_rt.so

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

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

other attached packages:
[1] xlsx_0.6.5 edgeR_3.36.0 limma_3.50.0
[4] corrplot_0.92 ggpubr_0.4.0 DESeq2_1.34.0
[7] SummarizedExperiment_1.24.0 Biobase_2.54.0 MatrixGenerics_1.6.0
[10] matrixStats_0.61.0 chromVAR_1.16.0 GenomicRanges_1.46.1
[13] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3
[16] BiocGenerics_0.40.0 viridis_0.6.2 viridisLite_0.4.0
[19] ggplot2_3.3.5 stringr_1.4.0 dplyr_1.0.7

loaded via a namespace (and not attached):
[1] colorspace_2.0-2 ggsignif_0.6.3 rjson_0.2.21
[4] ellipsis_0.3.2 XVector_0.34.0 rstudioapi_0.13
[7] DT_0.20 bit64_4.0.5 AnnotationDbi_1.56.2
[10] fansi_1.0.2 splines_4.1.0 R.methodsS3_1.8.1
[13] cachem_1.0.6 geneplotter_1.72.0 jsonlite_1.7.3
[16] Rsamtools_2.10.0 seqLogo_1.60.0 rJava_1.0-5
[19] broom_0.7.12 annotate_1.72.0 GO.db_3.14.0
[22] png_0.1-7 R.oo_1.24.0 shiny_1.7.1
[25] readr_2.1.2 compiler_4.1.0 httr_1.4.2
[28] backports_1.4.1 assertthat_0.2.1 Matrix_1.3-4
[31] fastmap_1.1.0 lazyeval_0.2.2 cli_3.1.1
[34] later_1.3.0 htmltools_0.5.2 tools_4.1.0
[37] gtable_0.3.0 glue_1.6.1 TFMPvalue_0.0.8
[40] GenomeInfoDbData_1.2.7 reshape2_1.4.4 Rcpp_1.0.8
[43] carData_3.0-5 vctrs_0.3.8 Biostrings_2.62.0
[46] rtracklayer_1.54.0 CNEr_1.30.0 xlsxjars_0.6.1
[49] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.1
[52] restfulr_0.0.13 poweRlaw_0.70.6 gtools_3.9.2
[55] rstatix_0.7.0 XML_3.99-0.8 zlibbioc_1.40.0
[58] scales_1.1.1 BSgenome_1.62.0 hms_1.1.1
[61] promises_1.2.0.1 parallel_4.1.0 RColorBrewer_1.1-2
[64] yaml_2.2.2 memoise_2.0.1 gridExtra_2.3
[67] stringi_1.7.6 RSQLite_2.2.9 genefilter_1.76.0
[70] BiocIO_1.4.0 caTools_1.18.2 BiocParallel_1.28.3
[73] rlang_1.0.1 pkgconfig_2.0.3 bitops_1.0-7
[76] pracma_2.3.6 lattice_0.20-45 purrr_0.3.4
[79] GenomicAlignments_1.30.0 htmlwidgets_1.5.4 bit_4.0.4
[82] tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.2
[85] R6_2.5.1 generics_0.1.2 DelayedArray_0.20.0
[88] DBI_1.1.2 pillar_1.7.0 withr_2.4.3
[91] survival_3.2-13 KEGGREST_1.34.0 abind_1.4-5
[94] RCurl_1.98-1.5 tibble_3.1.6 crayon_1.4.2
[97] car_3.0-12 utf8_1.2.2 plotly_4.10.0
[100] tzdb_0.2.0 TFBSTools_1.32.0 locfit_1.5-9.4
[103] grid_4.1.0 data.table_1.14.2 blob_1.2.2
[106] digest_0.6.29 xtable_1.8-4 tidyr_1.2.0
[109] httpuv_1.6.5 R.utils_2.11.0 munsell_0.5.0
[112] DirichletMultinomial_1.36.0

[janemd2012]

Never mind! I figure it out. Since there are more than one functions called the getCounts.

adding package info can make it work(:

test_counts <- chromVAR::getCounts(test_rg, peaks = test_peaks, by_rg = TRUE)