regionCounts() from csaw - object 'fancy_mseq' not found
0
0
Entering edit mode
zgraytho88 • 0
@766e7408
Last seen 4 months ago
United States

Hello,

I am trying to use the regionCounts() function from the csaw package and am receiving the following error:

Error in unlist_as_integer(x@subscript) : object 'fancy_mseq' not found

Any ideas?

Below is my code as representative as possible and session info:

chrs <- paste0("chr", c(1:19, "X", "Y"))
param <- readParam(pe="both", restrict=chrs, max.frag=600)

bam_files <- c("directory/bam1","directory/bam2","directory/bam3","directory/bam4")

ref_peak <- read.delim(bed_file, stringsAsFactors=FALSE, header=FALSE)
ref_peak <- GRanges(seqnames=ref_peak $V1, ranges=IRanges(ref_peak $V2+1, ref_peak $V3), id=ref_peak $V4)

reg.counts <- regionCounts(bam_files, ref_peak, ext=450, param=param)

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.2 (Ootpa)

Matrix products: default
BLAS:   /R/4.2.0/lib64/R/lib/libRblas.so
LAPACK: /R/lib/libRlapack.so

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    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1               stringr_1.4.0               dplyr_1.0.9                 purrr_0.3.4                 readr_2.1.2                
 [6] tidyr_1.2.0                 tibble_3.1.6                ggplot2_3.3.5               tidyverse_1.3.1             statmod_1.4.36             
[11] edgeR_3.38.0                limma_3.52.0                csaw_1.30.0                 SummarizedExperiment_1.26.0 Biobase_2.56.0             
[16] MatrixGenerics_1.8.0        matrixStats_0.62.0          GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1             
[21] S4Vectors_0.34.0            BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
 [1] httr_1.4.2             jsonlite_1.8.0         modelr_0.1.8           assertthat_0.2.1       cellranger_1.1.0       GenomeInfoDbData_1.2.4
 [7] Rsamtools_2.12.0       yaml_2.3.5             pillar_1.7.0           backports_1.4.1        lattice_0.20-45        glue_1.6.2            
[13] digest_0.6.29          XVector_0.30.0         rvest_1.0.2            colorspace_2.0-3       htmltools_0.5.2        Matrix_1.4-1          
[19] pkgconfig_2.0.3        broom_0.8.0            haven_2.5.0            zlibbioc_1.36.0        scales_1.2.0           tzdb_0.3.0            
[25] BiocParallel_1.30.0    generics_0.1.2         ellipsis_0.3.2         withr_2.5.0            cli_3.3.0              readxl_1.4.0          
[31] magrittr_2.0.3         crayon_1.5.1           evaluate_0.15          fs_1.5.2               fansi_1.0.3            xml2_1.3.3            
[37] tools_4.2.0            hms_1.1.1              lifecycle_1.0.1        reprex_2.0.1           munsell_0.5.0          locfit_1.5-9.5        
[43] DelayedArray_0.22.0    Biostrings_2.64.0      compiler_4.2.0         rlang_1.0.2            grid_4.2.0             RCurl_1.98-1.6        
[49] rstudioapi_0.13        bitops_1.0-7           rmarkdown_2.14         gtable_0.3.0           DBI_1.1.2              R6_2.5.1              
[55] lubridate_1.8.0        knitr_1.39             fastmap_1.1.0          utf8_1.2.2             metapod_1.4.0          stringi_1.7.6         
[61] parallel_4.2.0         Rcpp_1.0.8.3           vctrs_0.4.1            dbplyr_2.1.1           tidyselect_1.1.2       xfun_0.30

Thank you for any and all help!

ATACSeq regionCounts csaw • 400 views
ADD COMMENT
1
Entering edit mode

Does that also happen when you run the example section from regionCounts()? Seems to be related to S4vectors https://github.com/Bioconductor/S4Vectors/commit/07a75c72b6654d510f52d31ad0975fc24a67fa91

ADD REPLY
0
Entering edit mode

Thank you very much! This was very helpful in giving me direction!

ADD REPLY

Login before adding your answer.

Traffic: 235 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6