getMetadata_GeneByNeighbor_RnaSeq: getMetadata_GeneByNeighbor_RnaSeq

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

Get the metadata about the gene(s) within a given range.

Usage

getMetadata_GeneByNeighbor_RnaSeq(theStartPosition, theStopPosition, theChromosome, theStrand, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag = FALSE)

Arguments

theStartPosition	Inclusive position to start search.
theStopPosition	Inclusive position to stop search.
theChromosome	Chromosome (as string) to search, such as "X", "Y", "1", or "21" - NULL skips.
theStrand	Strand as a string "+" or "-" - NULL skips
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 "/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip". NOTE: this is a subdirectory of GENE_REPORT.
theVerboseFlag	Default: FALSE. TRUE means write all output, which can be very verbose.

Value

The return value is a list of objects with gene data. The following functions work to pull data out of the object.

get.GeneSymbol	get.GeneSymbol
get.GeneId	get.GeneId
get.VersionIndex	get.VersionIndex
get.LocationStart	get.LocationStart
get.LocationEnd	get.LocationEnd
get.Chromosome	get.Chromosome
get.Strand	get.Strand

Examples

#print(getMetadata_Gene_RnaSeq("?|100130426"))
#print(getMetadata_Gene_RnaSeq2("?|26823"))
#print(getMetadata_Gene_RnaSeq("A1BG"))
#print(getMetadata_Gene_RnaSeq2("tAKR"))
#print(getMetadata_Gene_RnaSeq("foo"))
#print(getMetadata_Gene_RnaSeq2("SNORD116-19"))
#print(getMetadata_Gene_RnaSeq("CT45A4"))
#print(getMetadata_GeneByNeighbor_RnaSeq(53700000, 53800000, "12", "-"))
#print(getMetadata_GeneByNeighbor_RnaSeq2(53700000, 53800000, "12", "+"))

GeneSurvey/TCGAGeneReport documentation built on May 6, 2019, 6:27 p.m.