blineShift | Shift the baseline to 0 |
check_tcpl_db_schema | Function that checks if the most recent v3 table schema is used in the database schema |
Configure functions | Functions for configuring the tcpl package |
flareFunc | Calculate the weighted mean of a square to detect plate flares |
Hill model utilites | Functions to solve the Hill model |
interlaceFunc | Calculate the weighted mean of a square to detect interlace effect |
invitrodb_dd | Short descriptions of fields for different tables are stored in a data dictionary. |
is.odd | Check for odd numbers |
Load assay information | Functions for loading assay information |
load_data_columns | Lists of column names returned from tcplLoadData invitrodb v4.1 (same as CCTE Bioactivity API version). |
lu | Abbreviation for 'length(unique(x))' |
lw | Abbreviation for 'length(which(x))' |
mc1 | Perform level 1 multiple-concentration processing |
mc2 | Perform level 2 multiple-concentration processing |
MC2_Methods | List of level 2 multiple-concentration correction functions |
mc2_mthds | List of level 2 multiple-concentration correction functions |
mc3 | Perform level 3 multiple-concentration processing |
MC3_Methods | List of level 3 multiple-concentration normalization methods |
mc3_mthds | List of level 3 multiple-concentration normalization methods |
mc4 | Perform level 4 multiple-concentration processing |
MC4_Methods | List of level 4 multiple-concentration methods for calculating bmad |
mc4_mthds | List of level 4 multiple-concentration methods for calculating bmad |
mc5 | Perform level 5 multiple-concentration processing |
MC5_Methods | Load list of level 5 multiple-concentration cutoff methods |
mc5_mthds | Load list of level 5 multiple-concentration cutoff methods |
mc6 | Perform level 6 multiple-concentration processing |
MC6_Methods | Load list of level 6 multiple-concentration flag methods |
mc6_mthds | Load list of level 6 multiple-concentration flag methods |
mcdat | A subset of ToxCast data showing changes in the activity of the intracellular estrogen receptor. |
mc_test | List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for mc data. |
mc_vignette | List with multi-concentration data for the vignette |
Method functions | Functions for managing processing methods |
Models | Model objective functions |
mthd_list_defaults | Lists of data frames returned from tcplMthdList invitrodb v4.2 |
Query functions | Wrappers for sending queries and fetching results |
Register/update annotation | Functions for registering & updating annotation information |
registerMthd | Add a new analysis method |
sc1 | Perform level 1 single-concentration processing |
SC1_Methods | List of level 1 single-concentration normalization functions |
sc1_mthds | List of level 1 single-concentration normalization functions |
sc2 | Perform level 2 single-concentration processing |
SC2_Methods | List of level 2 single-concentration hit-call functions |
sc2_mthds | List of level 2 single-concentration hit-call functions |
scdat | A subset of ToxCast data showing changes in transcription factor activity for multiple targets. |
sc_test | List of lists containing queries sent to tcplQuery associated with each test case. Each list also contains the associated ids with each case. Only meant to be used with automated testing with mocking for sc data. |
sc_vignette | List with single-concentration data for the vignette |
sink.reset | Reset all sinks |
tcplAddModel | Draw a tcpl Model onto an existing plot |
tcplAICProb | Calculate the AIC probabilities |
tcplAppend | Append rows to a table |
tcplCascade | Do a cascading delete on tcpl screening data |
tcplCode2CASN | Convert chemical code to CAS Registry Number |
tcplConf | Functions for configuring the tcpl package |
tcplConfDefault | Functions for configuring the tcpl package |
tcplConfList | Functions for configuring the tcpl package |
tcplConfLoad | Functions for configuring the tcpl package |
tcplConfReset | Functions for configuring the tcpl package |
tcplConfSave | Functions for configuring the tcpl package |
tcplCytoPt | Calculate the cytotoxicity point based on the "burst" endpoints |
tcpldbStats | Get summary statistics for the database |
tcplDefine | Load data dictionary descriptions |
tcplDelete | Delete rows from tcpl databases |
tcplFit | Fit the data with the constant, hill, and gain-loss models |
tcplFit2 | tcpl Wrapper for tcplfit2_core including additional calculations to fit into new schema |
tcplFit2_nest | Nest dataframe into a list that is readable by tcplfit2 |
tcplFit2_unnest | Unnest tcplfit2 parameters into a dataframe |
tcplGetAeid | get Aeid for endpoint name |
tcplggplot | tcplggplot |
tcplggplotCompare | tcplggplotCompare |
tcplHillACXX | Functions to solve the Hill model |
tcplHillConc | Functions to solve the Hill model |
tcplHillVal | Functions to solve the Hill model |
tcplHit2 | Hitcalling with tcplfit2 |
tcplLegacyPlot | tcplLegacyPlot |
tcplListFlds | Load the field names for a table |
tcplLoadAcid | Functions for loading assay information |
tcplLoadAeid | Functions for loading assay information |
tcplLoadAid | Functions for loading assay information |
tcplLoadAsid | Functions for loading assay information |
tcplLoadChem | Load sample/chemical information |
tcplLoadChemList | Load chemical list information |
tcplLoadConcUnit | Load concentration units for assay endpoints |
tcplLoadData | Load tcpl data |
tcplLoadUnit | Load response units for assay endpoints |
tcplLvlCount | Load tcpl level counts |
tcplMakeAeidMultiPlts | Create a .pdf with all dose-response plots for a given aeid, 6 per page |
tcplMakeAeidPlts | Create a .pdf with dose-response plots |
tcplMakeChidMultiPlts | Create a .pdf with all dose-response plots for a given chid, 6 per page |
tcplMthdAssign | Functions for managing processing methods |
tcplMthdClear | Functions for managing processing methods |
tcplMthdList | Functions for managing processing methods |
tcplMthdLoad | Functions for managing processing methods |
tcplMultiplot | Plot summary fits based on fit and dose-response data |
tcplObjCnst | Model objective functions |
tcplObjGnls | Model objective functions |
tcplObjHill | Model objective functions |
tcplPlot | #--- Generic Plotting Function for tcpl |
tcplPlotFitc | Plot the fit category tree |
tcplPlotFits | Plot summary fits based on fit and dose-response data |
tcplPlotLoadData | Utility function to load data for tcplPlot |
tcplPlotlyPlot | tcplPlotlyPlot |
tcplPlotM4ID | Plot fit summary plot by m4id |
tcplPlotPlate | Plot plate heatmap |
tcplPlotSetYRange | tcplPlotSetYRange |
tcplPlotValidate | tcplPlotValidate |
tcplPrepOtpt | Map assay/chemical ID values to annotation information |
tcplQuery | Wrappers for sending queries and fetching results |
tcplQueryAPI | Wrappers for sending queries and fetching results |
tcplRegister | Functions for registering & updating annotation information |
tcplRun | Perform data processing |
tcplSendQuery | Wrappers for sending queries and fetching results |
tcplSubsetChid | Subset level 5 data to a single sample per chemical |
tcplUpdate | Functions for registering & updating annotation information |
tcplVarMat | Create chemical by assay matrices |
tcplWriteData | Write screening data into the tcpl databases |
tcplWriteLvl0 | Write level 0 screening data into the tcpl databases |
test_api | List containing ids used for different automated tests of tcpl integration with the CTX APIs, randomly selected from what is available via API. |
write_lvl_4 | Write level 4 with updated schema |
.buildAssayQ | Generate query for assay information |
.convertNames | Convert assay names to their abbreviations |
.load6DR | Load data for tcpl6 |
.plateHeat | Plot plate heatmap |
.prepField | Paste appropriate table name to field name |