consensus_table: Generate a consensus table between a BAM alignment and a...
In gschofl/porequal: Assessing the quality of high-throughput multiple sequence alignments.
Description
Usage
Arguments
Details
Value
View source: R/alignment-quality.R
Description
Generate a consensus table between a BAM alignment and a reference sequence.
Usage
1
consensus_table(bamfile, reffile)
Arguments
bamfile
Path to the BAM file.
reffile
Path to the reference sequence (Fasta format).
Details
consensus_table generates a data.table with 5 columns:
The Position along the reference, the Nucleotide (A, C, G, T, or Gap [-]),
the number of reads at a Position for each Nucleotide, the
Value
A data.table. See Details.
gschofl/porequal documentation built on May 17, 2019, 8:53 a.m.
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Description Usage Arguments Details Value
View source: R/alignment-quality.R
Description
Generate a consensus table between a BAM alignment and a reference sequence.
Usage
1 | consensus_table(bamfile, reffile)
|
Arguments
bamfile |
Path to the BAM file. |
reffile |
Path to the reference sequence (Fasta format). |
Details
consensus_table generates a data.table with 5 columns:
The Position along the reference, the Nucleotide (A, C, G, T, or Gap [-]),
the number of reads at a Position for each Nucleotide, the
Value
A data.table. See Details.
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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