Hello!

When I run nearestTSS() from edgeR, it fails saying

> TSS <- nearestTSS(yall$genes$Chr, yall$genes$Locus, species="Hs")
Error in Out$distance[Out$neg] <- -Out$distance[Out$neg] : 
  NAs are not allowed in subscripted assignments

Here is the full code.

    R version 3.5.0 (2018-04-23) -- "Joy in Playing"
    Copyright (C) 2018 The R Foundation for Statistical Computing
    Platform: x86_64-pc-linux-gnu (64-bit)

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    > library(edgeR)
    Loading required package: limma
    > targets <- c("SRR097807_1_trimmed_bismark_bt2.bismark.cov.gz", "SRR097808_1_trimmed_bismark_bt2.bismark.cov.gz", "SRR097809_1_trimmed_bismark_bt2.bismark.cov.gz", "SRR097810_1_trimmed_bismark_bt2.bismark.cov.gz")
> ##read in bismark files
    > yall <- readBismark2DGE(targets, sample.names=targets)
    Reading SRR097807_1_trimmed_bismark_bt2.bismark.cov.gz 
    Reading SRR097808_1_trimmed_bismark_bt2.bismark.cov.gz 
    Reading SRR097809_1_trimmed_bismark_bt2.bismark.cov.gz 
    Reading SRR097810_1_trimmed_bismark_bt2.bismark.cov.gz 
    Hashing ...
    Collating counts ...
    > 
    > ##remove genomic segments that have not been assembled into recognizable chromosomes
    > keep <- rep(TRUE, nrow(yall))
    > Chr <- as.character(yall$genes$Chr)
    > keep[ grep("random",Chr) ] <- FALSE
    > keep[ grep("chrUn",Chr) ] <- FALSE
    > 
    > keep[Chr=="chrY"] <- FALSE
    > keep[Chr=="chrM"] <- FALSE
    > table(keep)
    keep
      FALSE    TRUE 
      17424 5971475 
    > 
    > ## subset DGEList to remove rows corresponding to unwanted chromosomes
    > ## keep.lib.sizes=FALSE cuases the library sizes to be recomputed
    > 
    > yall <- yall[keep,, keep.lib.sizes=FALSE]
    > ChrNames <- paste0("chr",c(1:22,"X"))
    > ChrNames
     [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
    [10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
    [19] "chr19" "chrX" 
    > yall$genes$Chr <- factor(yall$genes$Chr, levels=ChrNames)
    > o <- order(yall$genes$Chr, yall$genes$Locus)
    > yall <- yall[o,]
    > 
    > TSS <- nearestTSS(yall$genes$Chr, yall$genes$Locus, species="Hs")
    Error in Out$distance[Out$neg] <- -Out$distance[Out$neg] : 
      NAs are not allowed in subscripted assignments
    In addition: Warning message:
    replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘AnnotationDbi’ 
    > sessionInfo()
    R version 3.5.0 (2018-04-23)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: CentOS Linux 7 (Core)

    Matrix products: default
    BLAS: /opt/apps/r/3.5.0/lib64/R/lib/libRblas.so
    LAPACK: /opt/apps/r/3.5.0/lib64/R/lib/libRlapack.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] stats     graphics  grDevices utils     datasets  methods   base     

    other attached packages:
    [1] edgeR_3.24.0 limma_3.36.2

    loaded via a namespace (and not attached):
     [1] Rcpp_1.0.0           AnnotationDbi_1.44.0 BiocGenerics_0.28.0 
     [4] hms_0.4.2            IRanges_2.16.0       bit_1.1-14          
     [7] lattice_0.20-35      R6_2.2.2             rlang_0.3.0.1       
    [10] org.Hs.eg.db_3.7.0   blob_1.1.1           tools_3.5.0         
    [13] parallel_3.5.0       grid_3.5.0           Biobase_2.40.0      
    [16] DBI_1.0.0            bit64_0.9-7          digest_0.6.15       
    [19] tibble_1.4.2         readr_1.2.1          S4Vectors_0.20.1    
    [22] memoise_1.1.0        RSQLite_2.1.1        compiler_3.5.0      
    [25] pillar_1.2.3         stats4_3.5.0         locfit_1.5-9.1      
    [28] pkgconfig_2.0.1

What is causing this error? Thank you!