| rtfbs-package | Transcription Factor Binding Site Identification Tool |
| as.pointer.ms | MS To Pointer |
| build.mm | Build Markov Model to represent sequences in an MS object |
| calc.fdr | Calculate FDR |
| concat.ms | Concat MS |
| from.pointer.ms | MS From Pointer |
| gcContent.ms | Get GC content of each sequence in an MS object |
| groupByGC.ms | Group sequences by GC |
| is.pointer.ms | Data in R or C |
| label.matrix | Name PWM & MM rows and columns |
| length.ms | Length of MS object |
| lengths.ms | MS sequence lengths |
| makeFdrPlot | Plot FDR |
| ms | Multiple Sequence (MS) Objects |
| names.ms | MS Sequence Names |
| offsets.ms | Get index offsets |
| output.sites | Threshold possible binding sites by Score or FDR |
| print.ms | Prints an MS (multiple sequence) object. #' @title Printing MS objects |
| read.mm | Read Markov Model from file |
| read.ms | Reading in sequences from file |
| read.pwm | Read PWM object |
| rtfbs | Transcription Factor Binding Site Identification Tool |
| score.ms | Score sequences against a PWM |
| sequences.ms | Get sequences |
| simulate.ms | Generate sequence from Markov Model |
| split.ms | Split sequences |
| summary.ms | MS Summary |
| write.mm | Write Markov Model to file |
| write.ms | Writing MS Object to FASTA file |
| [.ms | Extract, replace, reorder MS |