gtoxPrepOtpt {GladiaTOX} | R Documentation |
gtoxPrepOtpt
queries the chemical and assay information from the gtox
database, and maps the annotation information to the given data.
gtoxPrepOtpt(dat, ids = NULL)
dat |
data.table, output from |
ids |
Character, (optional) a subset of ID fields to map |
gtoxPrepOtpt
is used to map chemical and assay identifiers to their
respective names and annotation information to create a human-readable table
that is more suitable for an export/output.
By default the function will map sample ID (spid), assay component id (acid), and assay endpoint ID (aeid) values. However, if 'ids' is not null, the function will only attempt to map the ID fields given by 'ids.'
The given data.table with chemical and assay information mapped
## Store the current config settings, so they can be reloaded at the end ## of the examples conf_store <- gtoxConfList() gtoxConfDefault() ## Load some example data d1 <- gtoxLoadData(1) ## Check for chemical name in 'dat' "chnm" %in% names(d1) ## FALSE ## Map chemical annotation only d2 <- gtoxPrepOtpt(d1, ids = "spid") "chnm" %in% names(d2) ## TRUE "acnm" %in% names(d2) ## FALSE ## Map all annotations d3 <- gtoxPrepOtpt(d1) ## Also works if function is given d2 "chnm" %in% names(d2) ## TRUE "acnm" %in% names(d2) ## FALSE ## Reset configuration options(conf_store)