build_model: Build Users' Own Model
In LncFinder: LncRNA Identification and Analysis Using Heterologous Features

Description Usage Arguments Details Value References Author(s) See Also Examples

This function is used to build new models with users' own data.

build_model(
  lncRNA.seq,
  mRNA.seq,
  frequencies.file,
  SS.features = FALSE,
  lncRNA.format = "DNA",
  mRNA.format = "DNA",
  parallel.cores = 2,
  folds.num = 10,
  seed = 1,
  gamma.range = (2^seq(-5, 0, 1)),
  cost.range = c(1, 4, 8, 16, 24, 32),
  ...
)

`lncRNA.seq`	Long non-coding sequences. Can be a FASTA file loaded by `seqinr-package` or secondary structure sequences file (Dot-Bracket Notation) obtained from function `run_RNAfold`. If `lncRNA.seq` is secondary structure sequences file, parameter `lncRNA.format` should be defined as `"SS"`.
`mRNA.seq`	mRNA sequences. FASTA file loaded by `read.fasta` or secondary structure sequences (Dot-Bracket Notation) obtained from function `run_RNAfold`. If `mRNA.seq` is secondary structure sequences file, parameter `mRNA.format` should be defined as `"SS"`.
`frequencies.file`	String or a list obtained from function `make_frequencies`. Input species name `"human"`, `"mouse"` or `"wheat"` to use pre-build frequencies files. Or assign a users' own frequencies file (Please refer to function `make_frequencies` for more information).
`SS.features`	Logical. If `SS.features = TRUE`, secondary structure features will be used to build the model. In this case, `lncRNA.seq` and `mRNA.seq` should be secondary structure sequences (Dot-Bracket Notation) obtained from function `run_RNAfold` and parameter `lncRNA.format` and `mRNA.format` should be set as `"SS"`.
`lncRNA.format`	String. Define the format of `lncRNA.seq`. `"DNA"` for DNA sequences and `"SS"` for secondary structure sequences. Only when both `mRNA.format` and `lncRNA.format` are set as `"SS"`, can the model with secondary structure features be built (`SS.features = TRUE`).
`mRNA.format`	String. Define the format of `mRNA.seq`. Can be `"DNA"` or `"SS"`. `"DNA"` for DNA sequences and `"SS"` for secondary structure sequences. When this parameter is defined as `"DNA"`, only the model without secondary structure features can be built. In this case, parameter `SS.features` should be set as `FALSE`.
`parallel.cores`	Integer. The number of cores for parallel computation. By default the number of cores is `2`, users can set as `-1` to run this function with all cores. During the process of svm tuning, if the number of `parallel.cores` is more than the `folds.num` (number of the folds for cross-validation), the number of `parallel.cores` will be set as `folds.num` automatically.
`folds.num`	Integer. Specify the number of folds for cross-validation. (Default: `10`)
`seed`	Integer. Used to set the seed for cross-validation. (Default: `1`)
`gamma.range`	The range of gamma. (Default: `2 ^ seq(-5, 0, 1)`)
`cost.range`	The range of cost. (Default: `c(1, 4, 8, 16, 24, 32)`)
`...`	Additional arguments passed to function `svm_tune` for customised SVM model training.

This function is used to build a new model with users' own sequences. Users can use function lnc_finder to predict the sequences with new models.

For the details of frequencies.file, please refer to function make_frequencies.

For the details of the features, please refer to function extract_features.

For the details of svm tuning, please refer to function svm_tune.

Returns a svm model.

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_frequencies, lnc_finder, extract_features, svm_tune, svm.

## Not run: 
data(demo_DNA.seq)
Seqs <- demo_DNA.seq

### Build the model with pre-build frequencies.file:
my_model <- build_model(lncRNA.seq = Seqs[1:5], mRNA.seq = Seqs[6:10],
                        frequencies.file = "human", SS.features = FALSE,
                        lncRNA.format = "DNA", mRNA.format = "DNA",
                        parallel.cores = 2, folds.num = 2, seed = 1,
                        gamma.range = (2 ^ seq(-5, -1, 2)),
                        cost.range = c(2, 6, 12, 20))

### Users can use default values of gamma.range and cost.range to find the
best parameters.
### Use your own frequencies file by assigning frequencies list to parameter
### "frequencies.file".

## End(Not run)