{ "_id": "6a1ade121d7bb097a09eb776", "Package": "PathoStat", "Type": "Package", "Title": "PathoStat Statistical Microbiome Analysis Package", "Version": "1.39.0", "Date": "2020-03-27", "Author": "Solaiappan Manimaran , Matthew\nBendall , Sandro Valenzuela Diaz\n, Eduardo Castro\n, Tyler Faits , Yue\nZhao , Anthony Nicholas Federico\n, W. Evan Johnson ", "Maintainer": "Solaiappan Manimaran , Yue Zhao\n", "Description": "The purpose of this package is to perform Statistical\nMicrobiome Analysis on metagenomics results from sequencing\ndata samples. In particular, it supports analyses on the\nPathoScope generated report files. 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table", "topics": [ "findRAfromCount" ] }, { "page": "findTaxonMat", "title": "Find the Taxonomy Information Matrix", "topics": [ "findTaxonMat" ] }, { "page": "findTaxonomy", "title": "Find the taxonomy for unlimited tids", "topics": [ "findTaxonomy" ] }, { "page": "findTaxonomy300", "title": "Find the taxonomy for maximum 300 tids", "topics": [ "findTaxonomy300" ] }, { "page": "Fisher_Test_Pam", "title": "Given PAM and disease/control annotation, do Chi-square test for each row of PAM", "topics": [ "Fisher_Test_Pam" ] }, { "page": "formatTaxTable", "title": "Format taxonomy table for rendering", "topics": [ "formatTaxTable" ] }, { "page": "GET_PAM", "title": "transform cpm counts to presence-absence matrix", "topics": [ "GET_PAM" ] }, { "page": "getShinyInput", "title": "Getter function to get the shinyInput option", "topics": [ "getShinyInput" ] }, { "page": "getShinyInputCombat", "title": "Getter function to get the shinyInputCombat option", "topics": [ "getShinyInputCombat" ] }, { "page": "getShinyInputOrig", "title": "Getter function to get the shinyInputOrig option", "topics": [ "getShinyInputOrig" ] }, { "page": "getSignatureFromMultipleGlmnet", "title": "Use Lasso to do feature selection", "topics": [ "getSignatureFromMultipleGlmnet" ] }, { "page": "grepTid", "title": "Greps the tid from the given identifier string", "topics": [ "grepTid" ] }, { "page": "loadPathoscopeReports", "title": "Loads all data from a set of PathoID reports. For each column in the PathoID report, construct a matrix where the rows are genomes and the columns are samples. Returns a list where each element is named according to the PathoID column. For example, ret[[\"Final.Best.Hit.Read.Numbers\"]] on the result of this function will get you the final count matrix. 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