Question: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct character list for `AA` column
0
gravatar for qliu7
18 months ago by
qliu70
Roswell Park Cancer Institute
qliu70 wrote:

Hi,

I have used both the SeqArray_1.19.0 and SeqArray_1.19.2, and the function of info() for the example gds data returned a list for the AA column, which does not seem correct. I remember it returned a characterList previous, but I am not sure which version it was. Could anyone please have any idea about it? or is this feature just intended? Thanks in advance!

Here are the codes and results:

 > file <- SeqArray::seqExampleFileName("gds")
 > file
 [1] "/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SeqArray/extdata/CEU_Exon.gds"
 > f <- SeqArray::seqOpen(file)
 > SeqArray::info(f)
 DataFrame with 1348 rows and 9 columns
             AA        AC        AN        DP       HM2       HM3          OR
         <list> <integer> <integer> <integer> <logical> <logical> <character>
 1    1,1,1,...         4       114      3251     FALSE     FALSE          NA
 2    T,G,A,...         1       106      2676     FALSE     FALSE          NA
 3    1,1,1,...         6       154      7610      TRUE      TRUE          NA
 4    T,G,A,...       128       146      3383      TRUE      TRUE          NA
 5    1,1,1,...        13       178      8362      TRUE      TRUE          NA
 ...        ...       ...       ...       ...       ...       ...         ...
 1344 T,G,A,...        11       138      1893     FALSE     FALSE          NA
 1345 1,1,1,...         2       162      1137     FALSE     FALSE          NA
 1346 T,G,A,...        11       142       823     FALSE     FALSE          NA
 1347 1,1,1,...         1       152      1257     FALSE     FALSE          NA
 1348 T,G,A,...         1         6        48     FALSE     FALSE          NA
               GP        BN
      <character> <integer>
 1      1:1115503       132
 2      1:1115548       132
 3      1:1120431        88
 4      1:3548136       100
 5      1:3548832       100
 ...          ...       ...
 1344 22:45312244       116
 1345 22:45312306       132
 1346 22:45312345       116
 1347 22:45312409       132
 1348 22:50616806       114

Here is the SessionInfo:

> sessionInfo()
 R Under development (unstable) (2017-11-30 r73804)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 16.04.3 LTS

 Matrix products: default
 BLAS: /home/qian/bin/R-devel/lib/libRblas.so
 LAPACK: /home/qian/bin/R-devel/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] parallel  stats4    stats     graphics  grDevices utils     datasets
 [8] methods   base

 other attached packages:
  [1] VariantExperiment_0.99.0   SummarizedExperiment_1.9.2
  [3] DelayedArray_0.5.9         matrixStats_0.52.2
  [5] Biobase_2.39.0             GenomicRanges_1.31.1
  [7] GenomeInfoDb_1.15.1        IRanges_2.13.4
  [9] S4Vectors_0.17.12          BiocGenerics_0.25.0
 [11] devtools_1.13.4

 loaded via a namespace (and not attached):
  [1] Rcpp_0.12.14            compiler_3.5.0          XVector_0.19.1
  [4] bitops_1.0-6            tools_3.5.0             zlibbioc_1.25.0
  [7] testthat_1.0.2          digest_0.6.12           memoise_1.1.0
 [10] lattice_0.20-35         Matrix_1.2-12           SeqArray_1.19.2
 [13] commonmark_1.4          GenomeInfoDbData_0.99.2 withr_2.1.0
 [16] stringr_1.2.0           roxygen2_6.0.1          xml2_1.1.1
 [19] Biostrings_2.47.0       desc_1.1.1              rprojroot_1.2
 [22] grid_3.5.0              R6_2.2.2                magrittr_1.5
 [25] backports_1.1.1         gdsfmt_1.15.0           assertthat_0.2.0
 [28] SNPRelate_1.13.1        stringi_1.1.6           RCurl_1.95-4.8
 [31] crayon_1.3.4

-- Qian

ADD COMMENTlink modified 18 months ago • written 18 months ago by qliu70
Answer: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
1
gravatar for zhengx
18 months ago by
zhengx30
United States
zhengx30 wrote:

It seems I should use .onLoad instead of .onAttach.

 

ADD COMMENTlink written 18 months ago by zhengx30
It works now with the SeqArray_1.19.5. Thanks!
ADD REPLYlink written 18 months ago by qliu70
Answer: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
0
gravatar for zhengx
18 months ago by
zhengx30
United States
zhengx30 wrote:

You should explicitly import the namespace of SeqArray.

please use library(SeqArray) or require(SeqArray)

 

 
ADD COMMENTlink written 18 months ago by zhengx30

Thanks for your reply. But I am writing a package and have imports the whole package of SeqArray. so it seems weird that when I use SeqArray::info, it does not call the correct function. I will look deeper into this and let you know if I still have question. Thanks!

ADD REPLYlink modified 18 months ago • written 18 months ago by qliu70
Answer: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
0
gravatar for Stephanie M. Gogarten
18 months ago by
University of Washington
Stephanie M. Gogarten640 wrote:

Something must have changed in devel in one of the packages SeqArray depends on. With SeqArray 1.9.4 but release versions of all its dependencies, SeqArray::info() still returns a CharacterList for AA. I will look into it, but I'm about to go on vacation so I won't have an answer for you until January.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Stephanie M. Gogarten640
1

qliu7 and I looked at this a bit. Here's a reproducible example.

gdsfile <- SeqArray::seqExampleFileName("gds")
gdsfile <- SeqArray::seqOpen(gdsfile)
xx <- .Call(SeqArray:::SEQ_GetData, gdsfile, "annotation/info/AA", FALSE)
names(xx)    ## NULL
library(SeqArray)
yy <- .Call(SeqArray:::SEQ_GetData, gdsfile, "annotation/info/AA", FALSE)
names(yy)   ## "length" "data"

The absence of names() on xx means that a different code path is take here. This is with

> packageVersion("SeqArray")
[1] '1.19.3'
> R.version.string
[1] "R Under development (unstable) (2017-12-09 r73876)"

I made a pull request.

 

ADD REPLYlink modified 18 months ago • written 18 months ago by Martin Morgan ♦♦ 23k

Thanks Martin for the quick debugging. 

ADD REPLYlink written 18 months ago by qliu70
Answer: SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct c
0
gravatar for qliu7
18 months ago by
qliu70
Roswell Park Cancer Institute
qliu70 wrote:

It works now with the SeqArray_1.19.5. Thanks for the fix~

ADD COMMENTlink written 18 months ago by qliu70
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