Dynamic Estimator of Microbial Communities

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Documentation for package ‘demic’ version 2.0.0

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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 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_ptrs_subset Get PTR estimates for output of the core pipeline on a subset of data
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
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
lme4_model Run mixed linear model with random effect using lme4
lm_column A convenient function for ordinary linear regression on two vectors
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