genes_to_granges {multicrispr}

R Documentation

Convert geneids into GRanges

Description

Convert geneids into GRanges

Usage

genes_to_granges(geneids, txdb, complement = TRUE, plot = TRUE, verbose = TRUE)

genefile_to_granges(file, txdb, complement = TRUE, plot = TRUE)

Arguments

geneids	Gene identifier vector
txdb	TxDb-class or EnsDb-class
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)

Value

GRanges-class

See Also

char_to_granges, bed_to_granges

Examples

# 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))

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