Man pages for demic
Dynamic Estimator of Microbial Communities
| compare_contig_subsets | Compares contig subset x against contig subset y |
| compare_sample_subsets | Compares sample subset x against sample subset y |
| consist_transfer | A function for data frame integration |
| ContigCluster1 | Contig Cluster 1 |
| ContigCluster2 | Contig Cluster 2 |
| contig_pca | A function to return the first dimension of PCA on an input... |
| cor_diff | Determine the majority orientation of the input PTR estimates... |
| df_transfer | A function for data frame transfer |
| est_ptr | Estimate PTRs using all input data as well as using subsets... |
| est_ptr_on | Tries up to max_attempts times to compare each permutation of... |
| est_ptr_on_all | Estimates PTRs based on the whole input dataset |
| est_ptrs_subset | Get PTR estimates for output of the core pipeline on a subset... |
| filter_sample | A function for sample filtration Input requirements: 1. have... |
| get_eptr_stats | Generate a variety of stats on PTR estimates for a given... |
| iterate_pipelines | A function for iteration of pipeline until convergence |
| ks | A convenient function for KS test of uniform distribution |
| lm_column | A convenient function for ordinary linear regression on two... |
| lme4_model | Run mixed linear model with random effect using lme4 |
| max_bin_001 | MaxBin2 Cluster 001 |
| max_bin_002 | MaxBin2 Cluster 002 |
| max_bin_003 | MaxBin2 Cluster 003 |
| pipeline | A function representing the pipeline of four steps including... |
| reshape_filtered | A function for reshape to facilitate PCA, removing all... |
| select_by_ks_test | A function to remove outlier contigs using KS test |
| test_reasonable | A function to test whether the result is reasonable |
| verify_input | Verify that the input dataframe/matrix is valid |
