I was using readRibodata to creat a riboData object It was fine when I used only the ribosomal data but it had an error when I also supplied the RNA-seq data.
Here is the code:
reps <- rep(c("WT", "KO"), each = 3) ribosamp <- paste0(reps, rep(1:3, time = 2)) ribofiles <- paste0("../kallisto/", ribosamp, "/pseudoalignments.sorted.dedup.bam") rnasamp <- paste0(reps, "I", rep(1:3, time = 2)) rnafiles <- paste0("../kallisto/", rnasamp, "/pseudoalignments.sorted.bam")
ribroDat <- readRibodata(ribofiles, rnaFiles = rnafiles, replicates = reps)
Here is the error medd\ssage:
Reading ribosomal files... ......done! Reading rna files...Error in .Call2("solveuserSEW0", start, end, width, PACKAGE = "IRanges") : solving row 2: range cannot be determined from the supplied arguments (too many NAs)
Could someone tell me how to solve this problem?
Regards, Hui
sessionInfo()
R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.so
locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C [3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8 [5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8 [7] LCPAPER=enUS.UTF-8 LCNAME=C [9] LCADDRESS=C LCTELEPHONE=C [11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] riboSeqR1.16.0 abind1.4-5 GenomicRanges1.34.0 [4] GenomeInfoDb1.18.2 IRanges2.16.0 S4Vectors0.20.1 [7] BiocGenerics0.28.0 ezlimmaplot0.0.1.9012 ezlimma0.2.3.9016 [10] RColorBrewer1.1-2 preprocessCore1.44.0 gplots3.0.1.1 [13] edgeR3.24.3 limma3.38.3 BiocManager1.30.4 [16] zeallot0.1.0 xfun0.7 roxygen26.1.1 [19] rmarkdown1.13 reshape21.4.3 readxl1.3.1 [22] magrittr1.5 knitr1.23 glue1.3.1 [25] usethis1.5.0 devtools2.0.2 forcats0.4.0 [28] stringr1.4.0 dplyr0.8.1 purrr0.3.2 [31] readr1.3.1 tidyr0.8.3 tibble2.1.3 [34] ggplot23.1.1 tidyverse_1.2.1
loaded via a namespace (and not attached): [1] nlme3.1-137 bitops1.0-6 fs1.3.1 [4] lubridate1.7.4 httr1.4.0 rprojroot1.3-2 [7] tools3.5.1 backports1.1.4 R62.4.0 [10] KernSmooth2.23-15 seqLogo1.48.0 lazyeval0.2.2 [13] colorspace1.4-1 withr2.1.2 tidyselect0.2.5 [16] prettyunits1.0.2 processx3.3.1 compiler3.5.1 [19] cli1.1.0 rvest0.3.4 xml21.2.0 [22] desc1.2.0 caTools1.17.1.2 scales1.0.0 [25] callr3.2.0 Rsamtools1.34.1 commonmark1.7 [28] digest0.6.19 XVector0.22.0 pkgconfig2.0.2 [31] htmltools0.3.6 sessioninfo1.1.1 baySeq2.16.0 [34] rlang0.3.4 rstudioapi0.10 generics0.0.2 [37] jsonlite1.6 BiocParallel1.16.6 gtools3.8.1 [40] RCurl1.95-4.12 GenomeInfoDbData1.2.0 Rcpp1.0.1 [43] munsell0.5.0 stringi1.4.3 zlibbioc1.28.0 [46] pkgbuild1.0.3 plyr1.8.4 grid3.5.1 [49] gdata2.18.0 crayon1.3.4 lattice0.20-35 [52] Biostrings2.50.2 haven2.1.0 hms0.4.2 [55] locfit1.5-9.1 ps1.3.0 pillar1.4.1 [58] pkgload1.0.2 evaluate0.14 remotes2.0.4 [61] modelr0.1.4 cellranger1.1.0 gtable0.3.0 [64] assertthat0.2.1 broom0.5.2 memoise1.1.0