Description Usage Arguments Details Value References Author(s) See Also Examples
This function can compute Euclidean Distance proposed by method LncFinder (Han et al. 2018). Euclidean Distance can be calculated on full sequence or the longest ORF region. The step and k of the sliding window can also be customized.
1 2 3 4 5 6 7 8 9 10 11 |
Sequences |
A FASTA file loaded by function |
label |
Optional. String. Indicate the label of the sequences such as "NonCoding", "Coding". |
referFreq |
a list obtained from function |
k |
An integer that indicates the sliding window size. (Default: |
step |
Integer defaulting to |
alphabet |
A vector of single characters that specify the different character
of the sequence. (Default: |
on.ORF |
Logical. If |
auto.full |
Logical. When |
parallel.cores |
Integer. The number of cores for parallel computation.
By default the number of cores is |
This function can compute Euclidean Distance proposed by LncFinder (HAN et al. 2018).
In LncFinder, two schemes are provided to calculate Euclidean Distance:
1) step = 3
and k = 6
on the longest ORF region;
2) step = 1
and k = 6
on full sequence.
Using this function compute_EucDistance
, both step
, k
,
and calculated region (full sequence or ORF)
can be customized to maximize its availability.
A dataframe.
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang & Ying Li. LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information, and physicochemical property. Briefings in Bioinformatics, 2019, 20(6):2009-2027.
HAN Siyu
make_referFreq
,
compute_LogDistance
,
compute_hexamerScore
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
Seqs <- seqinr::read.fasta(file =
"http://www.ncbi.nlm.nih.gov/WebSub/html/help/sample_files/nucleotide-sample.txt")
referFreq <- make_referFreq(cds.seq = Seqs, lncRNA.seq = Seqs, k = 6, step = 3,
alphabet = c("a", "c", "g", "t"), on.orf = TRUE,
ignore.illegal = TRUE)
data(demo_DNA.seq)
Sequences <- demo_DNA.seq
EucDistance <- compute_EucDistance(Sequences, label = "NonCoding", referFreq = referFreq,
k = 6, step = 3, alphabet = c("a", "c", "g", "t"),
on.ORF = TRUE, auto.full = TRUE, parallel.cores = 2)
## End(Not run)
|
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