createPWM: Create position weight matrix from multiple sequence...
In gschofl/DR2S: Dual redundant reference sequencing
Description
Usage
Arguments
Details
Value
Examples
Description
Create position weight matrix from multiple sequence alignment
Usage
1
Arguments
msa
A DNAStringSet object of aligned sequences.
indelRate
<numeric|NULL>; The estimated background rate of Indels.
Details
PWM: a matrix with position as row names and nucleotides as
column manes. Values are nucleotide weights at a position
A ConsensusMatrix is calculated from the MSA using
Biostrings::consensusMatrix and values are converted to probabilities.
Pseudocounts are added and values are divided by DNA probabilities and log2
score is reported
Value
A PWM matrix.
Examples
1
2
print("TODO: Add examples")
###
gschofl/DR2S documentation built on May 17, 2019, 8:40 a.m.
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Description Usage Arguments Details Value Examples
Description
Create position weight matrix from multiple sequence alignment
Usage
1 |
Arguments
msa |
A |
indelRate |
<numeric|NULL>; The estimated background rate of Indels. |
Details
PWM: a matrix with position as row names and nucleotides as
column manes. Values are nucleotide weights at a position
A ConsensusMatrix is calculated from the MSA using
Biostrings::consensusMatrix and values are converted to probabilities.
Pseudocounts are added and values are divided by DNA probabilities and log2
score is reported
Value
A PWM matrix.
Examples
1 2 | print("TODO: Add examples")
###
|
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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