rscu: Relative synonymous codon usage
In HVoltBb/kondonz: A Comprehensive Codon Analysis Toolbox
Description
Usage
Arguments
Details
Value
Description
Calculates the relative synomynous codon usage (RSCU) for each codon.
Usage
1
Arguments
x
a KZsqns object of codon sequence or a list of such objects
y
an optional number denoting the codon table to be used. 0 = standard codon table (default), 2 = vertibrate mitchodrial (See dna2aa for additional options). When an option other than those mentioned above is provided, the standard codon table will be used
stop
a optional boolean denoting whether the RSCU values for the stop codons should be returned. FALSE: NAs will be returned (default); TRUE: the RSCUs will be returned
supplementory.info
whether supplementory information should be returned. If TRUE, the top 5 and bottom 5 most frequently used codons will be returned in the result; if FALSE, no supplementory information will be returned, and this is the default option
Details
The RSCU is calculated for each animo acid coding codon present in the provided codon sequence. When any animo acid is missing from the sequence, each coding codon for that animo acid will have NA returned as their RSCU. The RSCU of stop codons also have NAs in their position as the default setting. To include RSCUs for the stop codons in the returned array, set stop as TRUE.
Value
a named list containing a numeric array of RSCUs for each animo acid, an ordered list the top 5 most frequently used codons, and an ordered list of the top 5 least frequently used codons. Or a list of such lists, when x is a list of objects
HVoltBb/kondonz documentation built on Jan. 11, 2020, 3:30 a.m.
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Description Usage Arguments Details Value
Description
Calculates the relative synomynous codon usage (RSCU) for each codon.
Usage
1 |
Arguments
x |
a KZsqns object of codon sequence or a list of such objects |
y |
an optional number denoting the codon table to be used. 0 = standard codon table (default), 2 = vertibrate mitchodrial (See dna2aa for additional options). When an option other than those mentioned above is provided, the standard codon table will be used |
stop |
a optional boolean denoting whether the RSCU values for the stop codons should be returned. FALSE: NAs will be returned (default); TRUE: the RSCUs will be returned |
supplementory.info |
whether supplementory information should be returned. If TRUE, the top 5 and bottom 5 most frequently used codons will be returned in the result; if FALSE, no supplementory information will be returned, and this is the default option |
Details
The RSCU is calculated for each animo acid coding codon present in the provided codon sequence. When any animo acid is missing from the sequence, each coding codon for that animo acid will have NA returned as their RSCU. The RSCU of stop codons also have NAs in their position as the default setting. To include RSCUs for the stop codons in the returned array, set stop as TRUE.
Value
a named list containing a numeric array of RSCUs for each animo acid, an ordered list the top 5 most frequently used codons, and an ordered list of the top 5 least frequently used codons. Or a list of such lists, when x is a list of objects
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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