View source: R/granges_conversion.R
df2GRanges | R Documentation |
Wrapper for GenomicRanges::makeGRangesFromDataFrame().
df2GRanges( geno, chr_name = "chr", start_name = "pos", end_name = "pos", strand_name = NULL, ref_version = ref_genome(), seq_lengths = NULL, is_circular = FALSE )
geno |
Data frame. |
chr_name |
Name of chromosome column. Default is 'chr'. |
start_name |
Name of start position column. Default is 'pos.' |
end_name |
Name of end position column. Default is 'pos' |
strand_name |
Name of end position column. Default is NULL. |
ref_version |
Reference genome version. Default is 'ref_genome()'. |
seq_lengths |
List of sequence lengths with sequence name as key. Default is NULL. |
is_circular |
Whether genome is circular. Default is FALSE. |
GenomicRanges::GRanges object.
geno = finemap("chr1", start = 5000000, end = 6000000, strain1 = c("C57BL_6J"), strain2 = c("AKR_J", "A_J", "BALB_cJ") ) geno$strand = "+" seq_lengths = stats::setNames( as.list(avail_chromosomes()$length), avail_chromosomes()$chr ) geno.granges = df2GRanges(geno, strand_name = "strand", seq_lengths = seq_lengths )
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