mmpa {mMPA} | R Documentation |
Number of Assays Required using Marker-Assisted Mini-Pooling with Algorithm (mMPA)
Description
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.
Usage
mmpa(v, s, K = 5, vf_cut = 1000, lod = 0, msg = T)
Arguments
v |
A vector of non-negative numerical assay results. |
s |
A vector of risk scores; |
K |
Pool size; default is |
vf_cut |
Cutoff value for defining positive cases;
default is |
lod |
A vector of lower limits of detection or a scalar if the limits are the
same; default is |
msg |
Message generated during calculation; default is |
Details
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.
Value
A vectorof length N%/%K
for the numbers of assays needed for all pools
that are formed.
References
Liu T, Hogan JW, Daniels, MJ, Coetzer M, Xu Y, Bove G, et al. Improved HIV-1 Viral Load Monitoring Capacity Using Pooled Testing with Marker-Assisted Deconvolution. Journal of AIDS. 2017;75(5): 580-587.
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.
See Also
Examples
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