ContigCluster1          Contig Cluster 1
ContigCluster2          Contig Cluster 2
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
contig_pca              A function to return the first dimension of PCA
                        on an input matrix
cor_diff                Determine the majority orientation of the input
                        PTR estimates correlations
df_transfer             A function for data frame transfer
est_ptr                 Estimate PTRs using all input data as well as
                        using subsets of contigs and samples
est_ptr_on              Tries up to max_attempts times to compare each
                        permutation of removing random subsets of
                        contigs/samples from X, and returns the PTR
                        estimate if a valid one comes back from the
                        comparisons
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 of data
filter_sample           A function for sample filtration Input
                        requirements: 1. have values in more than half
                        of the contigs 2. average log2(cov) > 0 in all
                        these contigs
get_eptr_stats          Generate a variety of stats on PTR estimates
                        for a given dataset
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 vectors
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 GC bias correction, sample
                        filtration, PCA and contig filtration
reshape_filtered        A function for reshape to facilitate PCA,
                        removing all contigs with missing values for
                        designated samples
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
