tcplCytoPt calculates the cytotoxicity point and average cytotoxicity
distribution based on the acitivty in the "burst" assay endpoints.
Integer, chemical ID values to subset on
Integer, assay endpoint ID values to override the "burst assay" definitions
Integer, mc6_mthd_id values to be passed to
Integer or Boolean, the number of tested assay endpoints required for a cheimcal to be used in calculating the "global MAD."
Numeric of length 1, the default cytotoxicity point value
tcplCytoPt provides estimates for chemical-specific cytotoxicity
distributions (more information available in the vignette.) Before
calculating the cytotoxicity distributions, the level 5 data is subsetted
The 'chid' parameter specifies a subset of chemicals to use in the
calculations, given by chemical ID (chid). The 'aeid' parameter specifies
which assays to use in calculating the cytotoxicity point and distribution.
tcplCytoPt will use all available chemicals and the
assay endpoints defined by the 'burst_assay' field in the
"assay_component_endpoint" table. The examples show how to identify the
tcplCytoPt returns the cytotoxicity point (the AC50 values of the
active "burst" endpoints), the corresponding MAD, and the global MAD (median
of the calculated MAD values). Not every chemical must be tested in every
"burst" endpoint. The 'min.test' parameter allows the user to specify a
minimum number of tested assay endpoints as a requirement for MAD values to
be included in the global MAD calculation. For example, suppose the user
supplies 10 "burst" assays. The user can choose to require a chemical to be
tested in at least 5 of those assays for it's MAD value to be included in
the global MAD calculation. Having chemicals with many less "burst" endpoints
tested may inflate or deflate the global MAD calculation. By default (values
tcplCytoPt requires a chemical to be
tested in at least 80% of the given "burst" assays. The user can also
provide 'min.test' values of
FALSE (indicating to include all MAD
values), or a number (indicating a specific number of endpoints).
Chemicals without at least 2 active "burst" assays do not have a MAD value, and the cytotoxicity point is defined by the 'default.pt' parameter. The default value for 'default.pt' is 3.
The resulting data.table has the following fields:
"chid" – The chemical ID.
"code" – The chemcial code.
"chnm" – The chemical name.
"casn" – The chemical CASRN.
"med" – The median of the "burst" endpoint log(AC50) ("modl_ga" in the level 5 output) values.
"mad" – The MAD of the "burst" endpoint log(AC50) values.
"ntst" – The number of "burst" endpoints tested.
"nhit" – The number of acive "burst" endpoints.
"use_global_mad" – TRUE/FALSE, whether the mad value was used in the global MAD calculation.
"global_mad" – The median of the "mad" values where "use_global_mad" is TRUE.
"cyto_pt" – The cytotoxicity point, or the value in "med" when "nhit" is at least 2.
"cyto_pt_um" – 10^cyto_pt
"lower_bnd_um" – 10^(cyto_pt - 3*global_mad)
A data.table with the cytotoxicity distribution for each chemical. The definition of the field names are listed under "details."
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
## Store the current config settings, so they can be reloaded at the end ## of the examples conf_store <- tcplConfList() tcplConfDefault() ## Load the "burst" endpoints -- none are defined in the example dataset tcplLoadAeid(fld = "burst_assay", val = 1) ## Calculate the cytotoxicity distributions using both example endpoints tcplCytoPt(aeid = 1:2) ## The above example does not calculate a global MAD, because no chemical ## hit both endpoints. (This makes sense, because both endpoints are ## derived from one component, where one endpoint is acitivity in the ## up direction, and the other is acitivty in the down direction.) ## Note, the cyto_pt is also 3 for all chemicals, because the function ## requires at least two endpoints to calculate a cytotoxicity point. If ## the user wishes to use one assay, this function is not necessary. ## Changing 'default.pt' will change cyto_pt in the resulting data.table tcplCytoPt(aeid = 1:2, default.pt = 6) ## Reset configuration options(conf_store)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.