inferCNVBayesNet {infercnv} | R Documentation

## inferCNVBayesNet: Run Bayesian Network Mixture Model To Obtain Posterior Probabilities For HMM Predicted States

### Description

Uses Markov Chain Monte Carlo (MCMC) and Gibbs sampling to estimate the posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM. Posterior probabilities are found for the entire CNV cluster and each individual cell line in the CNV.

### Usage

    inferCNVBayesNet(
      file_dir,
      infercnv_obj,
      HMM_states,
      out_dir,
      resume_file_token,
      model_file = NULL,
      CORES = 1,
      postMcmcMethod = NULL,
      plotingProbs = TRUE,
      quietly = TRUE,
      diagnostics = FALSE,
      HMM_type = HMM_type,
      k_obs_groups = k_obs_groups,
      cluster_by_groups = cluster_by_groups,
      reassignCNVs = TRUE,
      no_plot = no_plot
    )

### Arguments

`file_dir` | Location of the directory of the inferCNV outputs.
`infercnv_obj` | InferCNV object.
`HMM_states` | InferCNV object with HMM states in expression data.
`out_dir` | (string) Path to where the output file should be saved to.
`resume_file_token` | (string) String token that contains some info on settings used to name files.
`model_file` | Path to the BUGS Model file.
`CORES` | Option to run parallel by specifying the number of cores to be used. (Default: 1)
`postMcmcMethod` | What actions to take after finishing the MCMC.
`plotingProbs` | Option for adding plots of Cell and CNV probabilities. (Default: TRUE)
`quietly` | Option to print descriptions along each step. (Default: TRUE)
`diagnostics` | Option to plot Diagnostic plots and tables. (Default: FALSE)
`HMM_type` | The type of HMM that was ra, either 'i3' or 'i6'. Determines how many state were predicted by the HMM.
`k_obs_groups` | Number of groups in which to break the observations. (default: 1)
`cluster_by_groups` | If observations are defined according to groups (ie. patients), each group of cells will be clustered separately. (default=FALSE, instead will use k_obs_groups setting)
`reassignCNVs` | (boolean) Given the CNV associated probability of belonging to each possible state, reassign the state assignments made by the HMM to the state that has the highest probability. (default: TRUE)
`no_plot` | (boolean) Option set by infercnv::run() for producing visualizations.

### Value

Returns a MCMC_inferCNV_obj and posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM.

### Examples

    data(infercnv_data_example)
    data(infercnv_annots_example)
    data(infercnv_genes_example)
    data(HMM_states)

    infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example,
                                                              gene_order_file=infercnv_genes_example,
                                                              annotations_file=infercnv_annots_example,
                                                              ref_group_names=c("normal"))

    out_dir = tempfile()
    infercnv_object_example <- infercnv::run(infercnv_object_example,
                                             cutoff=1,
                                             out_dir=out_dir,
                                             cluster_by_groups=TRUE,
                                             denoise=TRUE,
                                             HMM=TRUE,
                                             num_threads=2,
                                             no_plot=TRUE)
    mcmc_obj <- infercnv::inferCNVBayesNet(infercnv_obj      = infercnv_object_example,
                                           HMM_states        = HMM_states,
                                           file_dir          = out_dir,
                                           postMcmcMethod    = "removeCNV",
                                           out_dir           = out_dir,
                                           resume_file_token = "HMMi6.hmm_mode-samples",
                                           quietly           = TRUE,
                                           CORES             = 2,
                                           plotingProbs      = FALSE,
                                           diagnostics       = FALSE,
                                           HMM_type          = 'i6',
                                           k_obs_groups      = 1,
                                           cluster_by_groups = FALSE,
                                           reassignCNVs      = FALSE,
                                           no_plot           = TRUE)

[Package infercnv version 1.8.1 Index]