# Transcription Factor Binding Site Identification Tool

## Documentation for package ‘rtfbs’ version 0.3.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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