Man pages for BigelowLab/tetramers
Tetramer Analysis with Principle Component Analysis
| bind_tetra | Bind a list of tetra matrices to one matrix (n x 136) |
| blastHitText | Trim a blast hit description string to a particular length... |
| cexfun | Returns a numeric vector suitable of cex values for plot... |
| clean_sequence | Tidy an input FASTA string |
| decomposeContigNames | Parse the name of a contig |
| getBlastWindow | Retrieve the window specification from a window name. |
| getExplanation | Retrieve the normalized 'explanation' of variance for each PC... |
| get_pal | Returns the even-numbered color palette associated with the... |
| getTetramerRange | Compute pretty [xy] ranges for TetramerPCA data |
| input_name | Extract a name from a filename |
| is_odd | Test for oddness |
| makeCombinations | Create a vector of the default combinations of A, C, G and T |
| normalize_tetra | Normalize the tetra sequences |
| pca_tetra | Perform Principal Component Analysis on the normalized,... |
| pchfun | Returns a numeric vector suitable of pch values for plot... |
| plot_PCvPC | Plot one PCx vs PCy pairing |
| plot_tetramers | Plot the Tetramers results with our without blast annonations |
| read_blast_output | Read a blast xml output file |
| read_fastafile | Read a FASTA file and possibly tidy it |
| reduce_tetra | Reduce the tetra census table to include just the 136... |
| run_blast_app | Run blast and extract the results |
| select_outliers | Selects the outliers for PCs 1-nPC using a tidy-approach |
| tabulate_windows | Tabulate the tetramers within a window advanced by step |
| TETRA | A gobal variable to store defaults for the tetramerPCA. |
| Tetramers | A base container class for tetramer analysis |
| tetramers-package | tetramers |
| trimLegendText | trims input text vector to length and adds etc if needed in... |
| trim_QueryDef | Trim a blast query name to a reasonable length |
| write_tetra | Write all of the known results |
