Question: A Problem about seqnames() in GenomicRanges
0
gravatar for shangguandong1996
7 days ago by
shangguandong19960 wrote:

I come up with a problem when I run the function in the "An Introduction to the GenomicRanges Package"。

> library(GenomicRanges)
> gr1 <- GRanges(
+   seqnames = "chr2",
+   ranges = IRanges(103, 106),
+   strand = "+",
+   score = 5L, GC = 0.45)
> gr2 <- GRanges(
+   seqnames = c("chr1", "chr1"),
+   ranges = IRanges(c(107, 113), width = 3),
+   strand = c("+", "-"),
+   score = 3:4, GC = c(0.3, 0.5))
> grl <- GRangesList("txA" = gr1, "txB" = gr2)
> seqnames(grl)
RleList of length 2
$txA
factor-Rle of length 1 with 1 run
Error in nchar(str[ind]) : invalid multibyte string, element 1

I run again in another PC with same GenomicRanges version, and I still meet this problem. But I run with older version, this problem disapper.

Here is my version now

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936    LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                               LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0  IRanges_2.18.2       S4Vectors_0.22.0     BiocGenerics_0.30.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.30.0        compiler_3.6.0         XVector_0.24.0         tools_3.6.0            GenomeInfoDbData_1.2.1 RCurl_1.95-4.12       
[7] bitops_1.0-6 

The version with no problem is GenomicRanges_1.34.0 and 1.28.6

genomicranges • 72 views
ADD COMMENTlink written 7 days ago by shangguandong19960

I am unable to currently reproduce this. Could you try doing a BiocManager::valid() to make sure all dependent packages are up-to-date and if necessary BiocManager::install() and if it asks to update packages choose a for update all. Please try again and see if this corrects the issue, else please comment back here and we will try to investigate further.

ADD REPLYlink written 6 days ago by shepherl ♦♦ 1.5k

Thanks for your reply. Here is my BiocManager::valid() result

> BiocManager::valid()

* sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm10_1.4.0        BSgenome.Athaliana.TAIR.TAIR9_1.3.1000   
 [3] BSgenome_1.52.0                           Biostrings_2.52.0                        
 [5] XVector_0.24.0                            rtracklayer_1.44.4                       
 [7] TxDb.Athaliana.BioMart.plantsmart28_3.2.2 magrittr_1.5                             
 [9] TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0    GenomicFeatures_1.36.4                   
[11] AnnotationDbi_1.46.1                      Biobase_2.44.0                           
[13] GenomicRanges_1.36.1                      GenomeInfoDb_1.20.0                      
[15] IRanges_2.18.2                            S4Vectors_0.22.0                         
[17] BiocGenerics_0.30.0                      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2                  compiler_3.6.0              pillar_1.4.2               
 [4] BiocManager_1.30.4          prettyunits_1.0.2           bitops_1.0-6               
 [7] tools_3.6.0                 zlibbioc_1.30.0             progress_1.2.2             
[10] zeallot_0.1.0               biomaRt_2.40.4              digest_0.6.20              
[13] bit_1.1-14                  lattice_0.20-38             RSQLite_2.1.2              
[16] memoise_1.1.0               tibble_2.1.3                pkgconfig_2.0.2            
[19] rlang_0.4.0                 Matrix_1.2-17               DelayedArray_0.10.0        
[22] DBI_1.0.0                   rstudioapi_0.10             GenomeInfoDbData_1.2.1     
[25] httr_1.4.1                  stringr_1.4.0               vctrs_0.2.0                
[28] hms_0.5.1                   grid_3.6.0                  bit64_0.9-7                
[31] R6_2.4.0                    BiocParallel_1.18.1         XML_3.98-1.20              
[34] blob_1.2.0                  matrixStats_0.55.0          GenomicAlignments_1.20.1   
[37] Rsamtools_2.0.0             backports_1.1.4             SummarizedExperiment_1.14.1
[40] assertthat_0.2.1            stringi_1.4.3               RCurl_1.95-4.12            
[43] crayon_1.3.4               

Bioconductor version '3.9'

  * 1 packages out-of-date
  * 2 packages too new

create a valid installation with

  BiocManager::install(c(
    "kableExtra", "S4Vectors", "wesanderson"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 2 packages too new 

Then I run

  BiocManager::install(c(
    "kableExtra", "S4Vectors", "wesanderson"
  ), update = TRUE, ask = FALSE)

And now

> BiocManager::valid()
[1] TRUE

ADD REPLYlink written 6 days ago by shangguandong19960

But I still get

> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomeInfoDb
Warning messages:
1: package ‘GenomicRanges’ was built under R version 3.6.1 
2: package ‘S4Vectors’ was built under R version 3.6.1 
3: package ‘IRanges’ was built under R version 3.6.1 
> gr1 <- GRanges(
+   seqnames = "chr2",
+   ranges = IRanges(103, 106),
+   strand = "+",
+   score = 5L, GC = 0.45)
> gr2 <- GRanges(
+   seqnames = c("chr1", "chr1"),
+   ranges = IRanges(c(107, 113), width = 3),
+   strand = c("+", "-"),
+   score = 3:4, GC = c(0.3, 0.5))
> grl <- GRangesList("txA" = gr1, "txB" = gr2)
> grl
GRangesList object of length 2:
$txA 
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     score        GC
         <Rle> <IRanges>  <Rle> | <integer> <numeric>
  [1]     chr2   103-106      + |         5      0.45

$txB 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames  ranges strand | score  GC
  [1]     chr1 107-109      + |     3 0.3
  [2]     chr1 113-115      - |     4 0.5

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
> seqnames(grl)
RleList of length 2
$txA
factor-Rle of length 1 with 1 run
Error in nchar(str[ind]) : invalid multibyte string, element 1
ADD REPLYlink written 6 days ago by shangguandong19960

Wild guess, but does

Sys.setlocale("LC_ALL","C")

help? I don't have your issue, and changing my computer to Chinese (Simplified)_China.936 didn't cause the error, but it's worth a try.

ADD REPLYlink written 5 days ago by James W. MacDonald51k

Cool! It does work!

> Sys.setlocale("LC_ALL","C")
[1] "C"
> library(GenomicRanges)
> gr1 <- GRanges(
+      seqnames = "chr2",
+      ranges = IRanges(103, 106),
+      strand = "+",
+      score = 5L, GC = 0.45)
> gr2 <- GRanges(
+      seqnames = c("chr1", "chr1"),
+      ranges = IRanges(c(107, 113), width = 3),
+      strand = c("+", "-"),
+      score = 3:4, GC = c(0.3, 0.5))
> grl <- GRangesList("txA" = gr1, "txB" = gr2)
> seqnames(grl)
RleList of length 2
$txA
factor-Rle of length 1 with 1 run
  Lengths:    1
  Values : chr2
Levels(2): chr2 chr1

$txB
factor-Rle of length 2 with 1 run
  Lengths:    2
  Values : chr1
Levels(2): chr2 chr1
ADD REPLYlink written 5 days ago by shangguandong19960
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