genes_to_granges {multicrispr} | R Documentation |
Convert geneids into GRanges
genes_to_granges(geneids, txdb, complement = TRUE, plot = TRUE, verbose = TRUE) genefile_to_granges(file, txdb, complement = TRUE, plot = TRUE)
geneids |
Gene identifier vector |
txdb |
|
complement |
TRUE (default) or FALSE: add complementary strand? |
plot |
TRUE (default) or FALSE |
verbose |
TRUE (default) or FALSE |
file |
Gene identifier file (one per row) |
char_to_granges
, bed_to_granges
# Entrez #------- genefile <- system.file('extdata/SRF.entrez', package='multicrispr') geneids <- as.character(read.table(genefile)[[1]]) txdb <- getFromNamespace('TxDb.Mmusculus.UCSC.mm10.knownGene', 'TxDb.Mmusculus.UCSC.mm10.knownGene') (gr <- genes_to_granges(geneids, txdb)) (gr <- genefile_to_granges(genefile, txdb)) # Ensembl #-------- # txdb <- AnnotationHub::AnnotationHub()[["AH75036"]] # genefile <- system.file('extdata/SRF.ensembl', package='multicrispr') # geneids <- as.character(read.table(genefile)[[1]]) # (gr <- genes_to_granges(geneids, txdb)) # (gr <- genefile_to_granges(genefile, txdb))