search

vanmooylipidomics / LOBSTAHS

Git repository for the R package "LOBSTAHS" (Lipid and Oxylipin Biomarker Screening Through Adduct Hierarchy Sequences)
Other
8 stars 12 forks source link

Error object 'num_compounds.this_species' not found when generating custom database #6

Closed jamesrco closed 7 years ago

jamesrco commented 7 years ago

Posted for @hfredricks. User is encountering error

Error in FUN(newX[, i], ...) : 
  object 'num_compounds.this_species' not found

when attempting to generate a new database from custom .csv tables. Similar to error encountered by earlier user (issue https://github.com/vanmooylipidomics/LOBSTAHS/issues/2) when attempting to add a lipid class not accommodated by generateLOBdbase().

jamesrco commented 7 years ago

Error appears to be of same origin. @hfredricks is attempting to create a database that included some lipid species not yet accommodated by the generateLOBdbase() function. The time has come to fix the the package so users can fully define a new compound or lipid class using only the input tables, so that modifications do not need to be made to the generateLOBdbase() function every time a new compound is added. This will require the addition of a few new fields to the basic component definitions table (https://github.com/vanmooylipidomics/LOBSTAHS/blob/master/inst/doc/csv/LOBSTAHS_basic_component_matrix.csv) and some modifications to the function code that make it a bit more generic.

jamesrco commented 7 years ago

Fixes incorporated into new package version 1.1.2. Makes adding new lipid classes and compounds to custom databases much easier.

Available now on GitHub: https://github.com/vanmooylipidomics/LOBSTAHS/releases/tag/v1.1.2 and pushing soon to Bioconductor-devel

Directions and explanations in revised vignette: https://github.com/vanmooylipidomics/LOBSTAHS/blob/master/vignettes/LOBSTAHS.Rmd

hfredricks commented 7 years ago

Thanks Jamie!