plotReadPairCoverage | R Documentation |
This function takes as an input aligned read-pairs in BAM and plots coverage profile per breakpoint. Breakpoint positions are stored as part of a readName. e.g. readName__chr1-109148195-109148196__chr1_invDup_gorilla_roi4_1
plotReadPairCoverage(
bamfile,
mapq = 10,
filt.flag = 0,
min.read.len = 5000,
plot.ambig = FALSE,
plot.pairs = FALSE,
blacklist = NULL,
view.range = 1e+05
)
bamfile |
Bamfile with aligned reads. |
mapq |
Minimum mapping quality when importing from BAM files. |
filt.flag |
Filter out reads with given flag. |
min.read.len |
Minimum length of mapped reads to import. |
plot.ambig |
Bamfile with aligned reads. |
plot.pairs |
Bamfile with aligned reads. |
blacklist |
A |
view.range |
Bamfile with aligned reads. |
A ggplot
object.
David Porubsky
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