mismatch-utils: Tally processing low-level functions
In Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies
Description
Usage
Arguments
See Also
Description
Functions for processing position-specific base count tables (tallies)
and extracting mismatches counts.
Usage
1
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## low-level functions
selectStrand(x, strand = c("both", "plus", "minus"), idx = 1:ncol(x))
seqDepth(x)
callConsensus(counts, verbose = FALSE)
mismatchCount(counts, consensus, depth = rowSums(counts))
Arguments
x
Input object
strand
Which strand to return?
idx
Index of bases to consider (leave as is)
counts
Count matrix
verbose
Show warnings
consensus
Consensus sequence
depth
Sequencing depth for counts
.
See Also
comparativeMismatch
Rariant documentation built on Nov. 8, 2020, 6:56 p.m.
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Description Usage Arguments See Also
Description
Functions for processing position-specific base count tables (tallies) and extracting mismatches counts.
Usage
1 2 3 4 5 6 7 8 | ## low-level functions
selectStrand(x, strand = c("both", "plus", "minus"), idx = 1:ncol(x))
seqDepth(x)
callConsensus(counts, verbose = FALSE)
mismatchCount(counts, consensus, depth = rowSums(counts))
|
Arguments
x |
Input object |
strand |
Which strand to return? |
idx |
Index of bases to consider (leave as is) |
counts |
Count matrix |
verbose |
Show warnings |
consensus |
Consensus sequence |
depth |
Sequencing depth for counts |
.
See Also
comparativeMismatch
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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