chop_by_introns {plyranges} | R Documentation |
Group a GRanges object by introns or gaps
chop_by_introns(x) chop_by_gaps(x)
x |
a GenomicRanges object with a cigar string column |
Creates a grouped Ranges object from a cigar string
column, for chop_by_introns()
will check for the presence of
"N" in the cigar string and create a new column called
intron
where TRUE indicates the alignment has a skipped
region from the reference. For chop_by_gaps()
will check
for the presence of "N" or "D" in the cigar string and
create a new column called "gaps" where TRUE indicates
the alignment has a deletion from the reference or has an intron.
a GRanges object
if (require(pasillaBamSubset)) { bamfile <- untreated1_chr4() # define a region of interest roi <- data.frame(seqnames = "chr4", start = 5e5, end = 7e5) %>% as_granges() # results in a grouped ranges object rng <- read_bam(bamfile) %>% filter_by_overlaps(roi) %>% chop_by_gaps() # to find ranges that have gaps use filter with `n()` rng %>% filter(n() > 2) }