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Table 2 isma user interface

From: isma: an R package for the integrative analysis of mutations detected by multiple pipelines

Function name Description
pre_process Read and integrate input files; generate unique identifiers
site_analysis Perform site-level analyses, calling get_sites_statistics, overlap_Tools, overlap_Subjects
gene_analysis Perform gene-level analyses, calling get_sites_statistics, overlap_Tools, overlap_Subjects, gene_mutation
site_annotation Perform site annotation
integrate_TCGA Integrate mutation evidence from TCGA
consensus_Tools Calculate the consensus among tools
get_sites_statistics* Calculate the co-occurrence of mutation sites/genes across callers and subjects
overlap_Subjects* Calculate subject-by-subject site/gene co-occurrence matrix
overlap_Tools* Calculate tool-by-tool site/gene co-occurrence matrix
ese_allsubj* Calculate the variation of site/genes amount and show the results for each tool
ese_tool_subj* Calculates the variation of site/genes amount, considering separately each tool and returns the results for each subject
ese_subj_tool* Calculates the variation of site amount, considering separately each subject and returns the results for each caller
calculate_dist_to_exon Calculate the site distance from the nearest exons
gene_mutation Calculate the gene-by-subject mutation matrix and the gene mutation frequency vectors
filtering_sites Filter sites
  1. The asterisk (*) indicates functions that work both at site- and gene-level