Question: MatchGenes in Bumphunter - result list with multiple genes
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4 months ago by
hanna_engqvist0 wrote:

Is it possible to get a result list with multiple genes per region using matchGenes in bumphunter? If yes, how? Is it also possible to output the start, end and chr in my input file. When I run the code below, I get only one gene per region even though UCSC genome browser shows multiple genes.

My code in R: BiocManager::install("bumphunter") library(bumphunter)

BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") library(TxDb.Hsapiens.UCSC.hg38.knownGene)

CNACCCMC<- read.csv("FindGeneSymbolTest.csv") CNACCCMC<-makeGRangesFromDataFrame(CNACCC_MC, keep.extra.columns=TRUE, start.field="start", end.field="end", seqnames.field="chr")

genome <- annotateTranscripts(TxDb.Hsapiens.UCSC.hg38.knownGene)

MatchGenesCCCMCTest <- matchGenes(CNACCCMC, genome, type = "any") write.csv(MatchGenesCCCMCTest, "MatchGenesCCCMC_Test.csv", row.names=FALSE)

Thank you in advance.

Kind regards, Hanna Engqvist

cancer • 71 views
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