sc_vignette: List with single-concentration data for the vignette

In tcpl: ToxCast Data Analysis Pipeline

List with single-concentration data for the vignette

Description

This dataset is a list with 3 data.tables (sc0,sc1,sc2).

Usage

sc_vignette

Format

1. sc0 A data frame with 10 rows and 18 columns containing level 0 formatted raw data.

   spid

   Sample ID

   chid

   Unique chemical ID number for tcpl

   casn

   Chemical Abstract Service(CAS) number

   chnm

   Chemical name

   dsstox_substance_id

   Chemical-specific DTXSID

   code

   CAS number compressed into numeric string

   acid

   Assay Component ID

   acnm

   Assay Component Name

   s0id

   Level 0 (sc0) ID

   apid

   Assay plate ID

   rowi

   Row Index

   coli

   Column Index

   wllt

   Well Type

   wllq

   Well Quality (0 or 1)

   conc

   Concentration in micromolar

   rval

   Raw assay component readout value

   srcf

   Source file containing the raw data

   conc_unit

   Concentration Units

2. sc1 A data frame with 10 rows and 20 columns containing level 1 normalized data.

   spid

   Sample ID

   chid

   Unique chemical ID number for tcpl

   casn

   Chemical Abstract Service(CAS) number

   chnm

   Chemical name

   dsstox_substance_id

   Chemical-specific DTXSID

   code

   CAS number compressed into numeric string

   aeid

   Assay Component Endpoint ID

   aenm

   Assay endpoint name (i.e., assay_component_endpoint_name)

   acid

   Assay Component ID

   acnm

   Assay Component Name

   s0id

   Level 0 (sc0) ID

   s1id

   Level 1 (sc1) ID

   apid

   Assay plate ID

   rowi

   Row Index

   coli

   Column Index

   wllt

   Well Type

   logc

   Log base 10 concentration

   resp

   Normalized response value

   resp_unit

   Response Units

   conc_unit

   Concentration Units

3. sc2 A data frame with 10 rows and 15 columns containing level 2 efficacy/hit designation data.

   spid

   Sample ID

   chid

   Unique chemical ID number for tcpl

   casn

   Chemical Abstract Service(CAS) number

   chnm

   Chemical name

   dsstox_substance_id

   Chemical-specific DTXSID

   code

   CAS number compressed into numeric string

   aeid

   Assay Component Endpoint ID

   aenm

   Assay endpoint name (i.e., assay_component_endpoint_name)

   s2id

   Level 2 (sc2) ID

   bmad

   The median absolute deviation of all treatment wells (default option) or blank wells

   max_med

   Maximum median response

   hitc

   Hitcall

   coff

   Cutoff

   resp_unit

   Response Units

   conc_unit

   Concentration Units

tcpl documentation built on Oct. 10, 2024, 1:07 a.m.