cnv_pipe: Calling CNV signature pipeline
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Value Author(s) See Also Examples

this pipeline integrate multiple independent steps in VSHunter.

cnv_pipe(CN_data, cores = 1, genome_build = c("hg19", "hg38"),
  de_novo = TRUE, reference_components = NULL, min_comp = 2,
  max_comp = 10, min_prior = 0.001, model_selection = "BIC",
  nrep = 1, niter = 1000, nTry = 12, ranks = NULL, nrun = 10,
  seed = 123456, plot_survey = TRUE,
  consensusmap_name = "nmf_consensus", testRandom = FALSE,
  nmfalg = "brunet", tmp = FALSE)

`CN_data`	a `QDNAseqCopyNumbers` object or a `list` contains multiple `data.frame`s (recommended), each `data.frame` stores copy-number profile for one sample with 'chromosome', 'start', 'end' and 'segVal' these four necessary columns. Of note, 'segVal' column shoule be absolute copy number values.
`cores`	number of compute cores to run this task. You can use `parallel::detectCores()` function to check how many cores you can use. If you are using `cnv_pipe()` feature, please do not use maximal number of cores in your computer, it may cause some unexpected problems.
`genome_build`	genome build version, must be one of 'hg19' or 'hg38'.
`de_novo`	default is `TRUE`. If set to `FALSE`, it will use reference components to generate sample-by-component matrix and then extract signatures.
`reference_components`	the object result from cnv_fitMixModels, default is `NULL`. When `de_novo` is `FALSE` and this argument is `NULL`, it will use reference components from Nature Genetics paper.
`min_comp`	minimal number of components to fit, default is 2.
`max_comp`	maximal number of components to fit, default is 10.
`min_prior`	minimal prior value, default is 0.001. Details about custom setting please refer to flexmix package.
`model_selection`	model selection strategy, default is 'BIC'. Details about custom setting please refer to flexmix package.
`nrep`	number of run times for each value of component, keep only the solution with maximum likelihood.
`niter`	maximal number of iteration to achive converge.
`nTry`	the maximal tried number of signatures, default is 12. Of note, this value should far less than number of features or samples.
`ranks`	a integer vector, manually specify `ranks` to capture instead of using auto-capture feature.
`nrun`	the number of run to perform for each value in range of 2 to `nTry`, default is 10. According to NMF package documentation, `nrun` set to 30~50 is enough to achieve robust result.
`seed`	seed number.
`plot_survey`	logical. If `TRUE`, plot rank survey.
`consensusmap_name`	a character, basename of consensus map output path.
`testRandom`	Should generate random data from input to test measurements. Default is `TRUE`.
`nmfalg`	specification of the NMF algorithm.
`tmp`	whether create a tmp directory to store temp result or not, default is `FALSE`.

a list contains results of NMF best rank survey, run, signature matrix, exposure list etc..

Shixiang Wang w_shixiang@163.com

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_generateSbCMatrix, cnv_getLengthFraction, cnv_plotDistributionProfile, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, cnv_quantifySigExposure, cnv_readprofile

## Not run: 
## load example copy-number data from tcga
load(system.file("inst/extdata", "example_cn_list.RData", package = "VSHunter"))
## run cnv signature pipeline
result = cnv_pipe(CN_data = tcga_segTabs, cores = 1, genome_build = "hg19")

## End(Not run)