getViewpointCoordinates {UMI4Cats} | R Documentation |
Finds the viewpoint coordinates for a given reference genome and sequence.
getViewpointCoordinates( bait_seq, bait_pad, res_enz, ref_gen, sel_seqname = NULL )
bait_seq |
Character containing the bait primer sequence. |
bait_pad |
Character containing the pad sequence (sequence between the bait primer and the restriction enzyme sequence). |
res_enz |
Character containing the restriction enzyme sequence. |
ref_gen |
A BSgenome object of the reference genome. |
sel_seqname |
A character with the chromosome name to focus the search for the viewpoint sequence. |
Creates a GRanges object containing the genomic position of the viewpoint.
getViewpointCoordinates( bait_seq = "GGACAAGCTCCCTGCAACTCA", bait_pad = "GGACTTGCA", res_enz = "GATC", ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19, sel_seqname = "chr16" # Look only in chr16 )