getMetadata_ProbeByNeighbor_Meth450: getMetadata_ProbeByNeighbor_Meth450

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

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

Usage

getMetadata_ProbeByNeighbor_Meth450(theStartPosition, theStopPosition, theChromosome, 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".
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

A list of probe objects, with names() as probe ids, as described in getMetadata_Probe_ functions. The following functions work to pull data out of the objects.

get.Name	get.Name
get.Chromosome	get.Chromosome
get.ProbeLocation	get.ProbeLocation
get.Strand	get.Strand
get.GeneStructure	get.GeneStructure

Examples

#getMetadata_ProbeByNeighbor_Meth450(7000000, 7005000, "X")

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