Dynamic Estimator of Microbial Communities

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Documentation for package ‘demic’ version 1.0.3

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combine_ests Combine output from the contigs pipeline and samples pipeline
compare_x_y Compares contig subset x against contig subset y
consist_transfer A function for data frame integration
ContigCluster1 Contig Cluster 1
ContigCluster2 Contig Cluster 2
contigs_pipeline Attempt the default iteration for contigs Requires at least 20 contigs
contig_pca A function to return the first dimension of PCA on an input matrix
cor_diff A function for orientation determination
df_transfer A function for data frame transfer
est_ptr Main function
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
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
rand_ordered_contigs Gives a randomly ordered set of contigs
reshape_filtered A function for reshape to facilitate PCA, removing all contigs with missing values for designated samples
samples_pipeline Attempt alternative iteration for samples Requires at least 3 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 input data meets pipeline criteria