Description Usage Arguments Value See Also Examples
View source: R/rfold_assembly_tx.R
rfold_assembly_tx
is used to assemble the output files of the RNAfold into a GRangesList object.
1 2 3 | 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)
|
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. |
A GRangesList
object, each element of it represents the MEA RNA structures in a transcript.
tx_seq_extraction
, RNAfold
, and Single_RNAfold
1 2 3 4 5 6 7 8 9 10 11 | ## 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)
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