Description Usage Arguments Details Value
View source: R/getTranscriptsAndExons.R
Get the transcripts for a particular gene
1 2 | getTranscripts_GeneSymbol_HG19(theGeneEq, theZipFile =
"/geneSurveyData/GeneSurvey.zip", theVerboseFlag = FALSE)
|
theGeneEq |
The gene symbol (or other entry from the HG19 data)– does not need to have the Ensembl id. If given just the symbol, all gene symbol|Ensembl ids will be returned. |
theZipFile |
Default: For DQS Servers. If you are on a server where the GENE_REPORT directory is on a different path, you can pass in a value to override the default of "/geneSurveyData/GeneSurvey.zip". |
theVerboseFlag |
Default: FALSE. TRUE means write all output, which can be very verbose. |
Collects all transcripts from the Ensembl definitions. All transcripts for the gene requested will be returned. See value for more details.
Returns a data.frame with the following colnames. "gene" The gene symbol|Ensembl id for this row, such as, TP53TG3|ENSG00000183632. "chromosome" The chromosome will be a number from 1 to 16 or an X or Y. "start" Start location for the Exon. "end" End location for the Exon. "strand" The + or - strand. "transcript_type" The transcript type such as "protein_coding" or "nonsense_mediated_decay". "transcript_id" The transcript id to which this Exon belongs, such as ENST00000398680. "transcript_symbol" The transcript symbol, a gene symbol, a dash, and an integer, such as TP53TG3-201.
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