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 |
open-brace.ms | Extract, replace, reorder MS |
output.sites | Threshold possible binding sites by Score or FDR |
print.ms | Prints an MS (multiple sequence) object. #' @title Printing... |
read.mm | Read Markov Model from file |
read.ms | Reading in sequences from file |
read.pwm | Read PWM object |
rtfbs-package | 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 |
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