TETRA: A gobal variable to store defaults for the tetramerPCA.
In BigelowLab/tetramers: Tetramer Analysis with Principle Component Analysis
TETRA R Documentation
A gobal variable to store defaults for the tetramerPCA.
Description
A gobal variable to store defaults for the tetramerPCA.
Usage
TETRA
Format
A list of global constants and defaults
- WINDOW
the window of analysis in bases - this windows 'slides' along the contig
- STEP
the distance in bases to advance the window between successive tabulations
- WIDTH
here it is always 4 bases per polymer, but the idea is that eventually other widths maybe possible
- NAME
currently unused
- NPC
The number of principle components to retain, by default 8
- CLEAN
logical, if TRUE then attempt to clean the inut contigs of disallowed characters
- VERBOSE
logical, if TRUE then output informational messages
- LOG
the name of the output log file, if used
- PICK
the number of outliers to select per PC, by default 2
- PAIRS
a two column matrix specifing the PCs to juxtapose
- BLASTPATH
the path to the location of the local install of blastn
- DNALETTERS
a list of allowed DNA letters
- TETRAMERS
a list of reverse-complimented tabulated tetramers, length = 136
- UTETRAMERS
a list of possible tetramers, some of which may be reverse compliments, length = 256
- FAILSTATUS
a list of reasons why a contig may fail the tetramerPCA process
- BLASTOPTS
a list of default blastn options
BigelowLab/tetramers documentation built on April 3, 2022, 8:22 p.m.
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.
| TETRA | R Documentation |
A gobal variable to store defaults for the tetramerPCA.
Description
A gobal variable to store defaults for the tetramerPCA.
Usage
TETRA
Format
A list of global constants and defaults
- WINDOW
the window of analysis in bases - this windows 'slides' along the contig
- STEP
the distance in bases to advance the window between successive tabulations
- WIDTH
here it is always 4 bases per polymer, but the idea is that eventually other widths maybe possible
- NAME
currently unused
- NPC
The number of principle components to retain, by default 8
- CLEAN
logical, if TRUE then attempt to clean the inut contigs of disallowed characters
- VERBOSE
logical, if TRUE then output informational messages
- LOG
the name of the output log file, if used
- PICK
the number of outliers to select per PC, by default 2
- PAIRS
a two column matrix specifing the PCs to juxtapose
- BLASTPATH
the path to the location of the local install of blastn
- DNALETTERS
a list of allowed DNA letters
- TETRAMERS
a list of reverse-complimented tabulated tetramers, length = 136
- UTETRAMERS
a list of possible tetramers, some of which may be reverse compliments, length = 256
- FAILSTATUS
a list of reasons why a contig may fail the tetramerPCA process
- BLASTOPTS
a list of default blastn options
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.