Transcription Factor Binding Site Identification Tool

Documentation for package ‘rtfbs’ version 0.3.15

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