geneSymbolsForDataset: geneSymbolsForDataset

In GeneSurvey/TCGAGeneReport: Access to Gene Report Data

Description

Take a vector of purported gene names and a vector of valid gene names and return a list containing matched and unmatched names. The matched names may also be corrected, such as when the RNASeq data adds a pipe and Entrez id to a gene symbol.

Usage

geneSymbolsForDataset(theRequestVector, theGeneSymbolVector)

Arguments

theRequestVector	Vector of purported gene symbols.
theGeneSymbolVector	Vector of valid gene symbols.

Details

Take a vector of purported gene symbol and a vector of valid gene names and return a list containing matched and unmatched names. The matched names may also be corrected, such as when the RNASeq data adds a pipe and Entrez id to a gene symbol.

This means a purported gene symbol of TP53 is returned as simply TP53, with a direct match. A purported gene symbol of FBXW7 is returned as matched to FBXW7|55294, since the TCGA Standardized Data from MD Anderson keeps the Entrez id, since the FBXW7 gene symbol was not in the translation file when this data set was processed. A purported gene symbol of FOO is returned as unmatched, since (at present) there is no such gene symbol.

Value

A list with two named elements, matched and unmatched. The matched components gives valid/known genes for the give gene list, while unmatched indicates genes for which no match was found.

Examples

## packageVector <- getNames_GeneSymbol_RnaSeq2()
## requestVector <- c("ZWINT", "TP53", "FBXW7", "FOO", "TBC1D3P1-DHX40P1")
## matches <- geneSymbolsForDataset(requestVector, packageVector)
## matches[[1]]
#[1] "ZWINT|11130"      "TP53"             "FBXW7|55294"      "TBC1D3P1-DHX40P1"
## matches[[2]]
#[1] "FOO"
## matches
#$matched
#[1] "ZWINT|11130"      "TP53"             "FBXW7|55294"      "TBC1D3P1-DHX40P1"
#
#$unmatched
#[1] "FOO"
#

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