Description Usage Arguments Value
Extract regions from a set of sequences (maybe with qualities)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | extract_region(
seq,
positions,
region,
region2 = region,
outfile = NULL,
append = FALSE,
format,
compress = NULL,
...
)
## S3 method for class 'character'
extract_region(
seq,
positions,
region,
region2 = region,
outfile = NULL,
append = FALSE,
format = NULL,
compress = NULL,
qualityType = "FastqQuality",
...
)
## S3 method for class 'XStringSet'
extract_region(
seq,
positions,
region,
region2 = region,
outfile = NULL,
append = FALSE,
format = NULL,
compress = NULL,
...
)
## S3 method for class 'ShortRead'
extract_region(
seq,
positions,
region,
region2 = region,
outfile = NULL,
append = FALSE,
format = NULL,
compress = NULL,
...
)
## S3 method for class 'list'
extract_region(seq, positions, region, region2 = region, outfile = NULL, ...)
|
seq |
( |
positions |
( |
region |
( |
region2 |
( |
outfile |
( |
append |
( |
format |
( |
compress |
( |
... |
Passed to methods. |
qualityType |
( |
(object
of the same class as seq
, or if seq
is a filename, XStringSet-class
or
QualityScaledXStringSet-class
depending on the
format of the file) The requested region from each of the input
sequences where it was found.
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