rfold_assembly_tx: Assembly of RNA secondary structures

In ZhenWei10/rBS2ndStructure: Filter the thermal stable RNA secondary structure

Description

rfold_assembly_tx is used to assemble the output files of the RNAfold into a GRangesList object.

Usage

rfold_assembly_tx(TXDB, Rfold_dir = "./", RfdNames = c("Fsm", "Fmd", "Flg"),
  DirNames = c("Small", "Middle", "Large"), small_threashold = 4500,
  middle_threashold = 8000, trim_wsize = 2000, trim_ssize = 1000)

Arguments

TXDB	The txdb object used to extract the transcripts.
Rfold_dir	The directory containing 3 sub-directories: "Small", "Middle", and "Large".
RfdNames	A character vector of length 3, which indicates the output names of the RNAfold used in 3 groups.
DirNames	A character vector of length 3, which indicates the directory names of the RNAfold used in 3 groups.
small_threashold	the transcript length threshold to put into the small group.
middle_threashold	the transcript length threshold to put into the middle group.
trim_wsize	the window size used for the trimming of the large group.
trim_ssize	the step size used for the trimming of the large group.

Value

A GRangesList object, each element of it represents the MEA RNA structures in a transcript.

See Also

tx_seq_extraction, RNAfold, and Single_RNAfold

Examples

## Not run:  
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
tx_seq_extraction(MMusculus,txdb,getwd()) 
RNAfold(1:30,"Small","Fsm") 
RNAfold(1:30,"Middle","Fmd") 
RNAfold(1:30,"Large","Flg") 
rfold_assembly_tx(txdb,RfdNames = c("Fsm","Fmd","Flg"))

## End(Not run)

ZhenWei10/rBS2ndStructure documentation built on Dec. 26, 2019, 3:37 a.m.