getExons_GeneSymbol_HG19: getExons_GeneSymbol_HG19
In MD-Anderson-Bioinformatics/GeneSurvey: MD Anderson Gene Survey

Description Usage Arguments Details Value

Get the exons for a particular gene

1 2	getExons_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 exons from the Ensembl definitions. All exons for 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. "exon_type" The exon type such as "protein_coding" or "nonsense_mediated_decay". "exon_id" The Ensembl Exon id such as ENSE00002304100. "exon_number" The exon number–an integer from 1 to number of exons. (Number can vary between traqnscripts.) "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.

MD-Anderson-Bioinformatics/GeneSurvey documentation built on May 7, 2019, 2:04 p.m.