Description Usage Arguments Value See Also Examples
tx_seq_extraction
is used to extract the fasta files of the full length transcripts.
1 2 3 4 5 | tx_seq_extraction(BS_genome, TXDB, Write_PATH = ".",
small_threashold = 4500, middle_threashold = 8000, trim_wsize = 2000,
trim_ssize = 1000, divide_num = 30)
newf(x)
|
BS_genome |
the |
TXDB |
the |
Write_PATH |
the path to write the transcript sequences. |
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 for the trimming. By default, only the transcripts in the large group are trimmed. |
trim_ssize |
the step size for the trimming. |
divide_num |
the number of fasta files divided for each of the 3 groups. This argument is useful when conducting the parallel computation of the |
This function will create 3 folders named Small, Middle, and Big. Each of them will contains a number of fasta files containing the full length transcripts of the sizes of each group.
The number of the fasta files is determined by the argument divide_num
.
RNAfold
, Single_RNAfold
, and rfold_assembly_tx
1 2 3 4 5 6 7 | ## 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())
## End(Not run)
|
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