qft.interp: Interpret the results of the Cellestis Quantiferon Gold...

In mmparker/tbdiag: Functions for Tuberculosis Diagnostics Research

Description

Given vectors of nil, TB antigen, and mitogen results in IU/mL, this function computes QFT qualitative interpretations. The function uses the Cellestis USA criterion by default; other criteria sets can be created as methods for the qft.criteria function.

Usage

qft.interp(nil, tb, mito, criteria = "cellestis.usa", verbosity = "terse",
  ...)

Arguments

nil	A vector of nil results (in IU/mL)
tb	A vector of TB antigen results (in IU/mL)
mito	A vector of mitogen results (in IU/mL)
criteria	The name of the desired result criteria (defaults to the Cellestis criteria for the United States).
verbosity	The level of verbosity ("onechar", "terse", "verbose") of the output.
...	Other arguments passed to the crtieria evaluation function chosen by the "criteria" argument.

Details

All IU/mL results greater than 10 are automatically censored to 10 for the purposes of calculating qualitative results, following Cellestis's interpretation instructions.

Value

The function returns a vector of qualitative assay results according to the criteria chosen using the "criteria" argument. The verbosity of the results depends on the value passed to the "verbosity" argument:

onechar	Returns a single character indicating the result (N for Negative, P for Positive, I for Indeterminate).
terse	Returns a single word indicating the result (Negative, Positive, Indeterminate).
verbose	Returns the same results as "terse", with the addition of a short comment indicating the reason for an "Indeterminate" result.

Multiple criteria sets are available. The function defaults to the standard Cellestis criteria for the United States of America (criteria = "cellestis.usa"), but other currently available options include:

criteria = "cellestis.nomito"	The Cellestis criteria for many regions outside of North America, in which indeterminate results are indicated for tests with high nil results, but not for tests with a Mitogen - Nil difference of less than 0.50 (as is the case in the US);
criteria = "070"	A criteria set in which the threshold for positivity is raised from Antigen - Nil = 0.35 to Antigen - Nil = 0.70, as has been suggested by some studies.

Note

This function is provided purely as a convenience and is not a replacement for manual interpretation, manufacturer-provided software, or common sense. Absolutely not for clinical use.

References

Cellestis <http://www.cellestis.com/>

See Also

tspot.interp for TSPOT.TB interpretation.

Examples

# Calculate results
test.qfts$result.check <- with(test.qfts,
                               qft.interp(nil = nil,
                                          tb = tb,
                                          mito = mito))

# Compare lab and calculated results
with(test.qfts, table(lab.result, result.check, exclude = NULL))

# Compare different levels of verbosity
test.qfts$verbose.check <- with(test.qfts,
                                qft.interp(nil = nil,
                                           tb = tb,
                                           mito = mito,
                                           verbosity = "verbose"))

test.qfts$onechar.check <- with(test.qfts,
                                qft.interp(nil = nil,
                                           tb = tb,
                                           mito = mito,
                                           verbosity = "onechar"))

unique(test.qfts[ , c("lab.result", "result.check",
                      "verbose.check", "onechar.check")])

mmparker/tbdiag documentation built on May 23, 2019, 5:05 a.m.