error in addIds

[AnnaSawicka]

Hi Mike, I have a problem with adding REFSEQ IDs to the SummarizedExperiment object, containing ENSEMBL transcripts and quantification information from Salmon. I have a tximeta_1.0.3 version. I used makeLinkedTxome:

indexPath <-"/usr/users/asawick/ania/U2OS_4sU_060319/salmon/Homo_sapiens.GRCh38.cdna.all_index" fastaPath <-"/usr/users/asawick/ania/U2OS_4sU_060319/salmon/Homo_sapiens.GRCh38.cdna.all.fa" gtfPath <- "/usr/users/asawick/ania/U2OS_4sU_060319/salmon/Homo_sapiens.GRCh38.96.gtf"

makeLinkedTxome(indexDir=indexPath, source="Ensembl", organism="Homo Sapiens", release="38", genome="GRCh", fasta=fastaPath, gtf=gtfPath, write=FALSE)

The object (st in this case) looks ok:

rowRanges(st) GRanges object with 168526 ranges and 6 metadata columns: seqnames ranges strand | tx_id

| ENST00000434970 14 22439007-22439015 + | ENST00000434970 ENST00000448914 14 22449113-22449125 + | ENST00000448914 ENST00000415118 14 22438547-22438554 + | ENST00000415118 ENST00000604446 15 21010494-21010516 - | ENST00000604446 ENST00000603693 15 21011451-21011469 - | ENST00000603693 ... ... ... ... . ... ENST00000635145 20 29878636-29879363 - | ENST00000635145 ENST00000617915 1 159972548-159974064 - | ENST00000617915 ENST00000455649 X 133989443-133990086 + | ENST00000455649 ENST00000278882 20 30377372-30399257 + | ENST00000278882 ENST00000644453 9 131370933-131372514 + | ENST00000644453 tx_biotype tx_cds_seq_start tx_cds_seq_end ENST00000434970 TR_D_gene 22439007 22439015 ENST00000448914 TR_D_gene 22449113 22449125 ENST00000415118 TR_D_gene 22438547 22438554 ENST00000604446 IG_D_gene 21010494 21010516 ENST00000603693 IG_D_gene 21011451 21011469 ... ... ... ... ENST00000635145 unprocessed_pseudogene ENST00000617915 unprocessed_pseudogene ENST00000455649 unprocessed_pseudogene ENST00000278882 unprocessed_pseudogene ENST00000644453 unprocessed_pseudogene gene_id tx_name ENST00000434970 ENSG00000237235 ENST00000434970 ENST00000448914 ENSG00000228985 ENST00000448914 ENST00000415118 ENSG00000223997 ENST00000415118 ENST00000604446 ENSG00000270824 ENST00000604446 ENST00000603693 ENSG00000270451 ENST00000603693 ... ... ... ENST00000635145 ENSG00000283020 ENST00000635145 ENST00000617915 ENSG00000273933 ENST00000617915 ENST00000455649 ENSG00000232068 ENST00000455649 ENST00000278882 ENSG00000149531 ENST00000278882 ENST00000644453 ENSG00000285287 ENST00000644453 ------- seqinfo: 47 sequences from GRCh38 genome

But I get the following error: library("org.Hs.eg.db")

st <-addIds(st, column = "REFSEQ", gene = F) Error in addIds(st, column = "REFSEQ", gene = F) : requireNamespace(orgpkg.name, quietly = TRUE) is not TRUE

Do you maybe know what I'm overlooking?

Thank you, Anna

[federicomarini]

Do you have the org.Hs.eg.db package installed? The error message seems to point at that.

[AnnaSawicka]

Thank for your quick response. yes, the package is installed. This is my sessionInfo, it's in "other attached packages" :

sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Scientific Linux 7.3 (Nitrogen)

Matrix products: default BLAS: /home/mpg05/asawick/tools/R-3.5.3/lib64/R/lib/libRblas.so LAPACK: /home/mpg05/asawick/tools/R-3.5.3/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] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.16.0 [4] S4Vectors_0.20.1 Biobase_2.42.0 BiocGenerics_0.28.0 [7] tximeta_1.0.3

[mikelove]

I'd prefer if we could switch to Bioconductor support site for these questions:

support.bioconductor.org

Please just post the above question and tag "tximeta"