isAdapter: Detect adapter contamination
In HTSeqGenie: A NGS analysis pipeline.
Description
Usage
Arguments
Value
View source: R/detectAdapterContam.R
Description
Does a Needleman-Wunsch like small-in-large alignment
of the adapter vs each read. Flag read if score exceeds threshold
Usage
1
isAdapter(reads, score_cutoff, adapter_seqs)
Arguments
reads
Set of reads as ShortRead object
score_cutoff
Alignment score threshold that needs to be exceeded to be flagged as adapter.
Usually this value is determined empirically by getAdpaterThreshold()
adapter_seqs
One or more adapter sequences
Value
boolean vector indicating adapter contamination
HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.
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Description Usage Arguments Value
View source: R/detectAdapterContam.R
Description
Does a Needleman-Wunsch like small-in-large alignment of the adapter vs each read. Flag read if score exceeds threshold
Usage
1 | isAdapter(reads, score_cutoff, adapter_seqs)
|
Arguments
reads |
Set of reads as ShortRead object |
score_cutoff |
Alignment score threshold that needs to be exceeded to be flagged as adapter. Usually this value is determined empirically by getAdpaterThreshold() |
adapter_seqs |
One or more adapter sequences |
Value
boolean vector indicating adapter contamination
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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