SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct character list for `AA` column
4
0
Entering edit mode
qliu7 • 0
@qliu7-13862
Last seen 18 months ago
Roswell Park Cancer Institute

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

SeqArray info SeqArray::info() • 2.0k views
ADD COMMENT
1
Entering edit mode
zhengx ▴ 30
@zhengx-7950
Last seen 4.9 years ago
United States

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

 

ADD COMMENT
0
Entering edit mode
It works now with the SeqArray_1.19.5. Thanks!
ADD REPLY
0
Entering edit mode
zhengx ▴ 30
@zhengx-7950
Last seen 4.9 years ago
United States

You should explicitly import the namespace of SeqArray.

please use library(SeqArray) or require(SeqArray)

 

 
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode
@stephanie-m-gogarten-5121
Last seen 9 days ago
University of Washington

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 COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

Thanks Martin for the quick debugging. 

ADD REPLY
0
Entering edit mode
qliu7 • 0
@qliu7-13862
Last seen 18 months ago
Roswell Park Cancer Institute

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

ADD COMMENT

Login before adding your answer.

Traffic: 884 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6