getMetadata_Gene_HG18: getMetadata_Gene_HG18

Description Usage Arguments Details Value Examples

View source: R/getMetadata_HG.R

Description

Get metadata about the given gene

Usage

1
getMetadata_Gene_HG18(theGene, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag = FALSE)

Arguments

theGene

A vector of gene symbols as found in the getNames_ function for this data type.

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.

Details

The getMetadata_gene functions return a list of sublists. The sublists will often contain only a single metadata object. However, the code is designed to handle multiple metadata objects for the same gene symbol. This is necessary for handling the multiple gene entries caused in various manners.

TCGA provided RNASeq (v1 and v2) gene mappings which are based on UCSC's transcripts data file and have "duplicate" "gene" entries. The "duplicates" are caused because the file in question, KnownGenes.txt, does not actually provide gene annotations. Instead of "genes", the file is measure transcript matches as generated by an automated, uncurated, system. This means wherever a match is "close enough", that part will be labeled with the matching gene, even if it does not match the NIH approved gene coordinates.

Other platforms, such as Methylation 27 and 450 and SNP6 which use the Gene Score algorithm have multiple entries for genes caused by alleles. These entries are current uniquely identified by adding first Chromosome and then some other identifier such as Entrez or Ensembl id to the gene symbol.

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

1
2
3
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

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