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CreateSQLiteIDs

For a subset of genes, create a file with additional reference IDs. Required for easy and efficient merging of TPdb info.

Version 0.1
Bundle sequencing
Categories DEG smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi)
Issue tracker View/Report issues
Requires biomaRt (R-bioconductor)
Source files component.xml SQLiteDB_xIDs.r
Usage Example with default values

Inputs

Name Type Mandatory Description
geneList CSV Mandatory Tab-delimited CSV file with headers and at least one column containing gene IDs to look up.

Outputs

Name Type Description
wIDs CSV Input file content with additional columns containing the listed reference IDs in the parameters.

Parameters

Name Type Default Description
attrTypes string "" Comma-separated list of associated gene IDs/attributes to retrieve.
biomart_dataset string "hsapiens_gene_ensembl" Ensembl biomart dataset to use.
keyCol string "" Column name of the input geneList to look up associated IDs for.
keyType string "ensembl_transcript_id" BiomaRt reference type of the keyCol. For reference, see a list of available attributes in hsapiens_gene_ensembl.
useMart_host string "" Genome build and version to pull references from. For example, "jun2013.archive.ensembl.org" retrieves IDs available in Ensembl 72. See Ensembl Archives to find the correct host URL.

Test cases

Test case Parameters IN
geneList
OUT
wIDs
case1 properties geneList wIDs

keyCol=mRNA,
attrTypes=entrezgene,refseq_mrna


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