Description Usage Arguments Details Value Examples
View source: R/TCGAGeneReport.R
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.
1 | geneSymbolsForDataset(theRequestVector, theGeneSymbolVector)
|
theRequestVector |
Vector of purported gene symbols. |
theGeneSymbolVector |
Vector of valid gene symbols. |
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.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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"
#
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