Entering edit mode
I am encountering an issue running totalCounts with multiple files. I get the following error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'nrow': attempt to apply non-function
Calls: totalCounts -> .addToTotal
The rest of the test code works fine, so it doesn't seem like an issue with the input files. Here is the test code:
library(rhdf5)
library(csaw)
library(diffHic)
library(edgeR)
hs.frag <- cutGenome("hg38.fa", "GATC", 4)
hs.param <- pairParam(hs.frag)
preparePairs("aligned_test1_REP1.bam", hs.param, file = "aligned_test1_REP1.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test1_REP2.bam", hs.param, file = "aligned_test1_REP2.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test2_REP2.bam", hs.param, file = "aligned_test2_REP2.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test2_REP1.bam", hs.param, file = "aligned_test2_REP1.h5", dedup = TRUE, minq=10)
input <- c("aligned_test1_REP1.h5", "aligned_test1_REP2.h5","aligned_test2_REP2.h5","aligned_test2_REP1.h5")
bin.size <- 1e6
data <- squareCounts(input, hs.param, width = bin.size, filter=1)
finder <- domainDirections(input, hs.param, width=1e5, span=10)
all.counts <- cbind(assay(finder, "up"), assay(finder, "down"))
totals <- totalCounts(input, hs.param)
sessionInfo():
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/openblas-0.3.8-2no6mfziiclwxb7lstxoos335gnhjpes/lib/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] edgeR_3.32.0 limma_3.46.0
[3] diffHic_1.24.0 InteractionSet_1.18.1
[5] csaw_1.24.3 SummarizedExperiment_1.20.0
[7] Biobase_2.50.0 MatrixGenerics_1.2.0
[9] matrixStats_0.57.0 GenomicRanges_1.42.0
[11] GenomeInfoDb_1.26.2 IRanges_2.24.1
[13] S4Vectors_0.28.1 BiocGenerics_0.36.0
[15] rhdf5_2.34.0
loaded via a namespace (and not attached):
[1] locfit_1.5-9.4 Rcpp_1.0.5 lattice_0.20-41
[4] prettyunits_1.1.1 Rsamtools_2.6.0 Biostrings_2.58.0
[7] assertthat_0.2.1 digest_0.6.27 BiocFileCache_1.14.0
[10] R6_2.5.0 RSQLite_2.2.2 httr_1.4.2
[13] pillar_1.4.7 zlibbioc_1.36.0 rlang_0.4.10
[16] GenomicFeatures_1.42.1 progress_1.2.2 curl_4.3
[19] blob_1.2.1 Matrix_1.3-2 BiocParallel_1.24.1
[22] Rhtslib_1.20.0 stringr_1.4.0 RCurl_1.98-1.2
[25] bit_4.0.4 biomaRt_2.46.0 DelayedArray_0.16.0
[28] compiler_4.0.3 rtracklayer_1.50.0 pkgconfig_2.0.3
[31] askpass_1.1 openssl_1.4.3 tidyselect_1.1.0
[34] tibble_3.0.4 GenomeInfoDbData_1.2.4 XML_3.99-0.5
[37] crayon_1.3.4 dplyr_1.0.2 dbplyr_2.0.0
[40] GenomicAlignments_1.26.0 bitops_1.0-6 rhdf5filters_1.2.1
[43] rappdirs_0.3.1 grid_4.0.3 lifecycle_1.0.0
[46] DBI_1.1.0 magrittr_2.0.1 stringi_1.5.3
[49] XVector_0.30.0 xml2_1.3.2 ellipsis_0.3.1
[52] generics_0.1.0 vctrs_0.3.6 Rhdf5lib_1.12.1
[55] tools_4.0.3 bit64_4.0.5 BSgenome_1.58.0
[58] glue_1.4.2 purrr_0.3.4 hms_0.5.3
[61] AnnotationDbi_1.52.0 memoise_1.1.0
This worked. Thank you so much for finding and fixing the problem so quickly!