narrowAlignments {CrispRVariants} | R Documentation |
Aligned reads are narrowed to the target region. In the case of reads with deletions spanning the boundaries of the target, reads are narrowed to the start of the deletion,
narrowAlignments(alns, target, ...) ## S4 method for signature 'GAlignments,GRanges' narrowAlignments(alns, target, ..., reverse.complement, minoverlap = NULL, verbose = FALSE, clipping.ops = c("S", "H"), match.ops = c("M", "X", "="))
alns |
A GAlignments object including a metadata column "seq" containing the sequence |
target |
A GRanges object |
... |
additional arguments |
reverse.complement |
Should the aligned reads be reverse complemented? |
minoverlap |
Minimum overlapping region between alignments and target. If not specified, alignments must span the entire target region. (Default: NULL) |
verbose |
(Default: FALSE) |
clipping.ops |
CIGAR operations corresponding to clipping (Default: c("S","H")) |
match.ops |
CIGAR operations corresponding to a match, i.e. a non-indel position (Default: c("M","X","=")) |
The narrowed alignments (GAlignments)
Helen Lindsay
bam_fname <- system.file("extdata", "gol_F1_clutch_2_embryo_4_s.bam", package = "CrispRVariants") bam <- GenomicAlignments::readGAlignments(bam_fname, use.names = TRUE) target <- GenomicRanges::GRanges("18", IRanges::IRanges(4647377, 4647399), strand = "+") narrowAlignments(bam, target, reverse.complement = FALSE)