Group a GRanges object by introns or gaps
chop_by_introns(x)
chop_by_gaps(x)a GenomicRanges object with a cigar string column
a GRanges object
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.
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)
}
#> GRanges object with 4258 ranges and 5 metadata columns:
#> Groups: gaps [2129]
#> seqnames ranges strand | which_label cigar
#> <Rle> <IRanges> <Rle> | <Rle> <character>
#> [1] chr4 501291-501317 - | chr4:500000-700000 27M84N48M
#> [2] chr4 501402-501449 - | chr4:500000-700000 27M84N48M
#> [3] chr4 501701-501767 - | chr4:500000-700000 67M67N8M
#> [4] chr4 501835-501842 - | chr4:500000-700000 67M67N8M
#> [5] chr4 501714-501767 - | chr4:500000-700000 54M67N21M
#> ... ... ... ... . ... ...
#> [4254] chr4 700351-700408 + | chr4:500000-700000 17M1291N58M
#> [4255] chr4 699050-699059 + | chr4:500000-700000 10M1291N65M
#> [4256] chr4 700351-700415 + | chr4:500000-700000 10M1291N65M
#> [4257] chr4 699050-699059 + | chr4:500000-700000 10M1291N65M
#> [4258] chr4 700351-700415 + | chr4:500000-700000 10M1291N65M
#> qwidth njunc gaps
#> <integer> <integer> <Rle>
#> [1] 75 1 22
#> [2] 75 1 22
#> [3] 75 1 55
#> [4] 75 1 55
#> [5] 75 1 56
#> ... ... ... ...
#> [4254] 75 1 26613
#> [4255] 75 1 26627
#> [4256] 75 1 26627
#> [4257] 75 1 26629
#> [4258] 75 1 26629
#> -------
#> seqinfo: 8 sequences from an unspecified genome