counterUMI4C {UMI4Cats} | R Documentation |
Algorithm for counting and collapsing the number of UMIs supporting a specific ligation.
counterUMI4C( wk_dir, pos_viewpoint, res_enz, digested_genome, filter_bp = 1e+07 )
wk_dir |
Working directory where to save the outputs generated by the UMI-4c analysis. |
pos_viewpoint |
GRanges object containing the genomic position of the viewpoint. |
res_enz |
Character containing the restriction enzyme sequence. |
digested_genome |
Path for the digested genome file generated using the
|
filter_bp |
Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6. |
For collapsing different molecules into the same UMI, takes into account the ligation position and the number of UMI sequence mismatches.
Creates a compressed tab-delimited file in wk_dir/count
named
"basename(fastq) _counts.tsv.gz
", containing the
coordinates for the viewpoint fragment, contact fragment and the number of
UMIs detected in the ligation.
if (interactive()) { path <- downloadUMI4CexampleData(reduced = TRUE) hg19_dpnii <- digestGenome( cut_pos = 0, res_enz = "GATC", name_RE = "DpnII", sel_chr = "chr16", # digest only chr16 to make example faster ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19, out_path = file.path(path, "digested_genome") ) viewpoint <- GenomicRanges::GRanges("chr16:10972515-10972548") counterUMI4C( wk_dir = file.path(path, "CIITA"), pos_viewpoint = viewpoint, res_enz = "GATC", digested_genome = hg19_dpnii ) }