calc_all_hmm_diff_parallel: HMM segmentation for each gene

In tinglab/redPATH: Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.

Description

HMM is inferred for a ON/HIGH and OFF/LOW state for each significant gene along a developmental pseudo time. Extension to a 3-state model is also provided.

Usage

calc_all_hmm_diff_parallel(sorted_gene_exprs_matrix, cls_num = 2,
  threadnum = 1)

Arguments

sorted_gene_exprs_matrix	Result returned from gene_selection function. A re-ordered gene by cell matrix
cls_num	The number of states for HMM. Defaults to 2.
threadnum	The number of threads to use.

Examples

dcor_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "dcor") 
mic_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "mic")
selected_result <- gene_selection(full_exprs_matrix, redpath_pseudotime, dcor_result, mic_result, threshold = 0.5)
gene_state_result <- calc_all_hmm_diff_parallel(selected_result, cls_num = 2, threadnum = 4)

tinglab/redPATH documentation built on May 31, 2019, 10:37 a.m.