Function_List.txt

check_clustering_on_tree.R
1. reverse_list_str() Reverse the structure of a list. Modified from https://stackoverflow.com/questions/15263146/revert-list-structure
2. get_largest_subtree() Called by check_tree_clustering to find largest pure subtrees
3. check_tree_clustering() Checks for clustering of an epi label on the phylogeny by comparing the number of isolates in a pure subtree between the real tree/data combination and trees with randomly permuted epi labels.

greatlakes_resource_usage.R
1. GetResourceUsage() Get memory usage and run time for a Great Lakes sbatch job given the job id
2. ConvertTimeToHours() Convert sbatch job run time into hours

parse_indels.R
1. get_indel_info_from_annotations() Grab information from each annotation
2. parse_indels() Parse indel variant matrix from Ali's pipeline

parse_snps.R
1. get_snp_info_from_annotations() Grab information from each annotation
2. parse_snps() Parse SNP matrix from Ali's pipeline

parse.R
1. remove_rows_with_bugs() Remove variant matrix rows with bugs in the annotations
2. remove_rows_with_no_variants_or_completely_masked() Remove rows with no variants or that are completely masked
3. split_rows_with_multiple_annots() Split rows that have multiple annotations
4. remove_rows_with_multiple_annots() Remove any rows with multiple annotations
5. remove_alt_allele_code_from_split_rows() Update code matrix such that alternative alleles are 0s
6. root_tree_og() Root tree on outgroup
7. get_anc_alleles() Get ancestral state of alleles
8. load_if_path() Load matrix from path if needed
9. remove_unknown_anc() Remove unknown ancestral states

reference_alleles.R
1. make_all_tree_edges_positive() Make tree edges positive
2. get_major_alleles() Get major alleles
3. remove_unknown_alleles() Remove unknown ancestral states
4. make_binary_matrix() Make binary matrix from allele matrix

validate.R
1. is_this_class() Tests if an input object has the specified class.
2. check_is_this_class() Checks if an object is of the expected R class.
3. check_is_tree() Check that the input tree is actually a 'phylo' object.
4. check_tree_is_rooted() Check that the tree has a root.
5. check_setequal_tree_mat() Confirm that the tree and variant matrix contain exactly the same samples