Question: In .get_cds_IDX(mcols0$type, mcols0$phase)
0
gravatar for yueli7
4 months ago by
yueli7140
China
yueli7140 wrote:

Hello,

Any one what is wrong with following message?

Thanks in advance for great help!

Best,

Yue

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
'select()' returned 1:many mapping between keys and columns



> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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     

loaded via a namespace (and not attached):
[1] compiler_3.6.1
rna-seq R • 175 views
ADD COMMENTlink modified 4 months ago by zx87549.2k • written 4 months ago by yueli7140

Provide your code and example data that produces these warnings/errors.

ADD REPLYlink written 4 months ago by zx87549.2k

Hello, zx8754,

Thank you so much for your suggestion! This is the same error in another question "Error: All columns in a tibble must be 1d or 2d objects:". so I close it.

Thank you again!

Best,

Yue

ADD REPLYlink modified 4 months ago • written 4 months ago by yueli7140
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