MultiAssayExperiment objects in the R programming language are used to store many assays all relatiing to one phenotype, project, goal, etc. - please see https://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html
However, presently the tools used for creating these objects, such as those housed by cBioPortalData, are crude and frequently fail
Herein, we hypothesize that this occurs because these tools are based on receiving appropriately formatted files as input. By contrast, the MaeUtils repository is founded on the tautology that the internal structure and logic of a Mae object provides substantial information as to whether a set of flatfiles is appopriate for instantiation of the same.
Specifically, we demonstrate a decreased failure rate in appropriate object construction that is founded on a series of heuristics designed to unambiguously identify the primaryId column that lays within the file best suited to become colData(MAE). The functions will attempt to identify such a column even in the absence of exact matches to the strings in a candidate column.
The first functionality (i.e., FlatFilesToMae.R) attempts to automate creation of Mae objects given only a directory containing (appropriatelt formatted) flat files as input. Future functonality to enhance ease of use is planned once this is done.