mMPA: Number of Assays Required using Marker-Assisted Mini-Pooling...
In taotliu/mMPA: Implementation of Marker-Assisted Mini-Pooling with Algorithm

Description Usage Arguments Details Value References See Also Examples

Function mmpa(...) calculates the number of assays required, when using mMPA, for pools that are formed following the order of individual samples in the data.

1	mmpa(v, s, K = 5, vf_cut = 1000, lod = 0, msg = T)

`v`	A vector of non-negative numerical assay results.
`s`	A vector of risk scores; `s` must have the same length as `v`. The risk score `s` needs to be positively associated with `v`; othewise an error message will be generated.
`K`	Pool size; default is `K = 5`.
`vf_cut`	Cutoff value for defining positive cases; default is `vf_cut = 1000`.
`lod`	A vector of lower limits of detection or a scalar if the limits are the same; default is `lod = 0`.
`msg`	Message generated during calculation; default is `TRUE`.

For a given sample (v_i, s_i), i = 1, ..., N, the first K samples are combined to form a pool, the next K samples are combined to form the second pool, and so on. If the number of samples for the last pool is less than K, these remaining samples are not used to form a pool (i.e. not included in the calculation) . Therefore, a total of N%/%K pools are formed. The function calculates the number of assays needed for each of these pools.

A vectorof length N%/%K for the numbers of assays needed for all pools that are formed.

Bilder CR, Tebbs JM, Chen P. Informative retesting. Journal of the American Statistical Association. 2010;105(491):942-955.

May S, Gamst A, Haubrich R, Benson C, Smith DM. Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection. Journal of Acquired Immune Deficiency Syndromes. 2010;53(2):194-201.

Our manuscript (under review); to be added.

minipool, mpa, pooling_mc

K=5; n = 50;
n.pool  = n/K; n.pool
#   [1] 10
set.seed(100)
pvl = rgamma(n, shape = 2.8, scale = 150)
riskscore = (rank(pvl)/n) * 0.5 + runif(n) * 0.5
mmpa(v = pvl, s = riskscore)
#   A total of 10 pools are formed.
#   The numbers of assays required by these pools are:
#   [1] 3 3 4 4 2 3 3 4 3 3